All studies
| ExclusiveBF | Non_exclusiveBF | No_BF | sum | |
|---|---|---|---|---|
| Bangladesh | 138 | 178 | 6 | 322 |
| Canada | 86 | 48 | 33 | 167 |
| Haiti | 37 | 11 | 0 | 48 |
| South Africa | 86 | 57 | 0 | 143 |
| USA(CA_FL) | 150 | 68 | 12 | 230 |
| USA(CA_MA_MO) | 38 | 66 | 116 | 220 |
| USA(NC) | 12 | 8 | 1 | 21 |
| All studies | 547 | 436 | 168 | 1151 |
All studies for stratified meta-analysis by birth mode
| Vaginal | C-section | sum | |
|---|---|---|---|
| Canada | 130 | 37 | 167 |
| Haiti | 42 | 6 | 48 |
| USA(CA_FL) | 162 | 65 | 227 |
| USA(CA_MA_MO) | 150 | 78 | 228 |
| All studies | 484 | 186 | 670 |
Grey color
Meta-analysis models based on adjusted estimate (adjusted for age of infant at sample collection) and standard error from linear mixed effect models.
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.5
Wood et al 2018 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.7
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.1
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.0
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 60.2
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 5.9
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.6
%W(random)
Thompson et al 2015 ( USA(NC) ) 7.3
Wood et al 2018 ( South Africa ) 13.4
Pannaraj et al 2017 ( USA(CA_FL) ) 18.7
Bender et al 2016 ( Haiti ) 8.7
Subramanian et al 2014 ( Bangladesh ) 21.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 14.5
Azad et al 2015 ( Canada ) 16.3
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1913 [0.1003; 0.2823] 4.12 < 0.0001
Random effects model 0.3336 [0.0894; 0.5778] 2.68 0.0074
Quantifying heterogeneity:
tau^2 = 0.0702; H = 2.06 [1.42; 2.98]; I^2 = 76.4% [50.4%; 88.8%]
Test of heterogeneity:
Q d.f. p-value
25.40 6 0.0003
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2018 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.5
Wood et al 2018 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.8
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.4
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 61.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 6.0
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.8
%W(random)
Thompson et al 2015 ( USA(NC) ) 8.1
Wood et al 2018 ( South Africa ) 14.8
Pannaraj et al 2017 ( USA(CA_FL) ) 20.4
Subramanian et al 2014 ( Bangladesh ) 22.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 15.9
Azad et al 2015 ( Canada ) 17.8
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1988 [0.1069; 0.2908] 4.24 < 0.0001
Random effects model 0.3835 [0.1247; 0.6422] 2.90 0.0037
Quantifying heterogeneity:
tau^2 = 0.0726; H = 2.20 [1.49; 3.25]; I^2 = 79.3% [54.7%; 90.5%]
Test of heterogeneity:
Q d.f. p-value
24.11 5 0.0002
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2018 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Wood et al 2018 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.8
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.4
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.0
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 61.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 6.0
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.7
%W(random)
Wood et al 2018 ( South Africa ) 14.3
Pannaraj et al 2017 ( USA(CA_FL) ) 20.4
Bender et al 2016 ( Haiti ) 9.1
Subramanian et al 2014 ( Bangladesh ) 23.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 15.5
Azad et al 2015 ( Canada ) 17.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1808 [0.0891; 0.2725] 3.87 0.0001
Random effects model 0.2909 [0.0458; 0.5360] 2.33 0.0200
Quantifying heterogeneity:
tau^2 = 0.0640; H = 2.10 [1.41; 3.13]; I^2 = 77.3% [49.6%; 89.8%]
Test of heterogeneity:
Q d.f. p-value
22.05 5 0.0005
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Wood et al 2018 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.6
Wood et al 2018 ( South Africa ) 0.1214 [-0.2963; 0.5390] 5.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 18.2
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.1
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 63.9
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 9.1
%W(random)
Thompson et al 2015 ( USA(NC) ) 7.4
Wood et al 2018 ( South Africa ) 15.0
Pannaraj et al 2017 ( USA(CA_FL) ) 22.8
Bender et al 2016 ( Haiti ) 9.0
Subramanian et al 2014 ( Bangladesh ) 26.7
Azad et al 2015 ( Canada ) 19.0
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1574 [0.0636; 0.2512] 3.29 0.0010
Random effects model 0.2602 [0.0267; 0.4936] 2.18 0.0290
Quantifying heterogeneity:
tau^2 = 0.0495; H = 1.83 [1.20; 2.80]; I^2 = 70.3% [30.5%; 87.3%]
Test of heterogeneity:
Q d.f. p-value
16.83 5 0.0048
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2018 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 2.0223 [ 1.0746; 2.9701] 23.9
Bender et al 2016 (Haiti) -0.5119 [-2.7851; 1.7614] 4.1
Pannaraj et al 2017 (USA(CA_FL)) 0.5934 [-0.0958; 1.2826] 45.1
Sordillo et al 2017 (USA(CA_MA_MO)) 1.5749 [ 0.6821; 2.4677] 26.9
%W(random)
Azad et al 2015 (Canada) 27.7
Bender et al 2016 (Haiti) 10.8
Pannaraj et al 2017 (USA(CA_FL)) 32.8
Sordillo et al 2017 (USA(CA_MA_MO)) 28.8
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 1.1523 [0.6894; 1.6152] 4.88 < 0.0001
Random effects model 1.1519 [0.2829; 2.0209] 2.60 0.0094
Quantifying heterogeneity:
tau^2 = 0.4763; H = 1.70 [1.00; 2.92]; I^2 = 65.4% [0.0%; 88.2%]
Test of heterogeneity:
Q d.f. p-value
8.68 3 0.0338
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 2.88635033937751e-05 |
| Bender et al 2016 (Haiti) | 0.658981004403214 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.0914811823311381 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.000545678208685348 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.6820 [-1.3391; 2.7031] 14.4
Bender et al 2016 (Haiti) -0.3508 [-4.3974; 3.6958] 3.6
Pannaraj et al 2017 (USA(CA_FL)) 0.7880 [-0.2996; 1.8755] 49.7
Sordillo et al 2017 (USA(CA_MA_MO)) 1.1977 [-0.1522; 2.5476] 32.3
%W(random)
Azad et al 2015 (Canada) 14.4
Bender et al 2016 (Haiti) 3.6
Pannaraj et al 2017 (USA(CA_FL)) 49.7
Sordillo et al 2017 (USA(CA_MA_MO)) 32.3
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.8641 [0.0971; 1.6310] 2.21 0.0272
Random effects model 0.8641 [0.0971; 1.6310] 2.21 0.0272
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.17]; I^2 = 0.0% [0.0%; 27.2%]
Test of heterogeneity:
Q d.f. p-value
0.63 3 0.8893
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.508396867999409 |
| Bender et al 2016 (Haiti) | 0.865079808120753 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.155598040795797 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.0820319111581724 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 (Bangladesh) 0.0308 [-0.0757; 0.1372] 44.1
Azad et al 2015 (Canada) 0.5818 [ 0.4102; 0.7534] 17.0
Pannaraj et al 2017 (USA(CA_FL)) 0.3161 [ 0.1504; 0.4819] 18.2
Sordillo et al 2017 (USA(CA_MA_MO)) 0.5214 [ 0.3626; 0.6802] 19.8
Thompson et al 2015 (USA(NC)) 0.2911 [-0.4807; 1.0628] 0.8
%W(random)
Subramanian et al 2014 (Bangladesh) 24.0
Azad et al 2015 (Canada) 22.6
Pannaraj et al 2017 (USA(CA_FL)) 22.7
Sordillo et al 2017 (USA(CA_MA_MO)) 22.9
Thompson et al 2015 (USA(NC)) 7.8
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.2758 [0.2051; 0.3465] 7.64 < 0.0001
Random effects model 0.3526 [0.0926; 0.6125] 2.66 0.0079
Quantifying heterogeneity:
tau^2 = 0.0703; H = 3.24 [2.28; 4.61]; I^2 = 90.5% [80.7%; 95.3%]
Test of heterogeneity:
Q d.f. p-value
41.99 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 (Bangladesh) | 0.570837554151296 |
| Azad et al 2015 (Canada) | 2.9999698377109e-11 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.000185565976276297 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 1.24192582145007e-10 |
| Thompson et al 2015 (USA(NC)) | 0.459754398037424 |
With GAMM fit and 95%CI.
Number of infants by duration of bf in the test set
<=2 months >2 months
26 13
Number of samples by duration of bf in the test set
<=2 months >2 months
483 252
Number of samples by duration of bf in the test set (>6 months only)
<=2 months >2 months
305 176
Grey
Test for age > 6 months and <15months GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.516456 | 0.4287802 | 26.858644 | 0.0000000 |
| month.exbf2>2 months | -1.634246 | 0.7401967 | -2.207854 | 0.0280084 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):month.exbf2<=2 months | 1.000001 | 1.000001 | 120.79393 | 0 |
| s(age.sample):month.exbf2>2 months | 1.000000 | 1.000000 | 60.88972 | 0 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.516456 | 0.4302022 | 264 | 26.769865 | 0.0000000 |
| Xmonth.exbf2>2 months | -1.634246 | 0.7426508 | 37 | -2.200557 | 0.0340874 |
| Xs(age.sample):month.exbf2<=2 monthsFx1 | 2.352653 | 0.2147700 | 264 | 10.954291 | 0.0000000 |
| Xs(age.sample):month.exbf2>2 monthsFx1 | 2.231823 | 0.2869630 | 264 | 7.777391 | 0.0000000 |
With GAMM fit and 95%CI.
Samples <= 6 months only
Samples <=6 months only
Subramanian (Bangladesh) data only.
Shannon index.
For samples <=6 months old only.
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0677 [-0.0136; 0.1491] 79.0
Azad et al 2015 ( Canada ) 0.3752 [ 0.0596; 0.6908] 5.3
Bender et al 2016 ( Haiti ) 0.4922 [-0.3266; 1.3110] 0.8
Wood et al 2018 ( South Africa ) 0.5113 [ 0.0923; 0.9303] 3.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1201 [-0.1362; 0.3764] 8.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.6457 [ 0.2430; 1.0485] 3.2
Thompson et al 2015 ( USA(NC) ) 0.4111 [-0.4054; 1.2277] 0.8
%W(random)
Subramanian et al 2014 ( Bangladesh ) 28.0
Azad et al 2015 ( Canada ) 16.8
Bender et al 2016 ( Haiti ) 4.9
Wood et al 2018 ( South Africa ) 12.6
Pannaraj et al 2017 ( USA(CA_FL) ) 19.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 13.2
Thompson et al 2015 ( USA(NC) ) 4.9
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1259 [0.0536; 0.1982] 3.41 0.0006
Random effects model 0.2995 [0.1020; 0.4969] 2.97 0.0030
Quantifying heterogeneity:
tau^2 = 0.0346; H = 1.59 [1.05; 2.41]; I^2 = 60.7% [9.9%; 82.8%]
Test of heterogeneity:
Q d.f. p-value
15.25 6 0.0184
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.102847325927163 |
| Azad et al 2015 ( Canada ) | 0.01980051110656 |
| Bender et al 2016 ( Haiti ) | 0.238756122389415 |
| Wood et al 2018 ( South Africa ) | 0.0167677830041401 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.358399385859461 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.00167635766494574 |
| Thompson et al 2015 ( USA(NC) ) | 0.32371285335117 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0673 [-0.0127; 0.1473] 77.1
Azad et al 2015 ( Canada ) 0.3721 [ 0.0590; 0.6852] 5.0
Bender et al 2016 ( Haiti ) 0.4601 [-0.3413; 1.2616] 0.8
Wood et al 2018 ( South Africa ) 0.4996 [ 0.0848; 0.9143] 2.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1447 [-0.0763; 0.3657] 10.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.6461 [ 0.2454; 1.0467] 3.1
Thompson et al 2015 ( USA(NC) ) 0.3555 [-0.3448; 1.0557] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 28.2
Azad et al 2015 ( Canada ) 16.1
Bender et al 2016 ( Haiti ) 4.5
Wood et al 2018 ( South Africa ) 12.0
Pannaraj et al 2017 ( USA(CA_FL) ) 21.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 12.5
Thompson et al 2015 ( USA(NC) ) 5.7
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1266 [0.0564; 0.1969] 3.53 0.0004
Random effects model 0.2909 [0.1053; 0.4765] 3.07 0.0021
Quantifying heterogeneity:
tau^2 = 0.0301; H = 1.59 [1.05; 2.41]; I^2 = 60.4% [9.1%; 82.7%]
Test of heterogeneity:
Q d.f. p-value
15.14 6 0.0192
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0990100956520888 |
| Azad et al 2015 ( Canada ) | 0.019839103185688 |
| Bender et al 2016 ( Haiti ) | 0.260501865374435 |
| Wood et al 2018 ( South Africa ) | 0.0182288177251842 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.19952096913775 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.00157427402976728 |
| Thompson et al 2015 ( USA(NC) ) | 0.319751771051308 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0953 [ 0.0196; 0.1710] 80.5
Azad et al 2015 ( Canada ) 0.2877 [-0.0327; 0.6082] 4.5
Bender et al 2016 ( Haiti ) 0.3082 [-0.3766; 0.9931] 1.0
Wood et al 2018 ( South Africa ) 0.4724 [ 0.0489; 0.8958] 2.6
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2168 [ 0.0121; 0.4215] 11.0
Thompson et al 2015 ( USA(NC) ) 0.7261 [-0.2385; 1.6906] 0.5
%W(random)
Subramanian et al 2014 ( Bangladesh ) 52.8
Azad et al 2015 ( Canada ) 12.0
Bender et al 2016 ( Haiti ) 3.1
Wood et al 2018 ( South Africa ) 7.4
Pannaraj et al 2017 ( USA(CA_FL) ) 23.2
Thompson et al 2015 ( USA(NC) ) 1.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1322 [0.0643; 0.2001] 3.82 0.0001
Random effects model 0.1910 [0.0685; 0.3134] 3.06 0.0022
Quantifying heterogeneity:
tau^2 = 0.0059; H = 1.15 [1.00; 1.78]; I^2 = 25.0% [0.0%; 68.4%]
Test of heterogeneity:
Q d.f. p-value
6.66 5 0.2469
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0136266394489582 |
| Azad et al 2015 ( Canada ) | 0.0784131649118116 |
| Bender et al 2016 ( Haiti ) | 0.377692577417145 |
| Wood et al 2018 ( South Africa ) | 0.0288048675369895 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0379096968161372 |
| Thompson et al 2015 ( USA(NC) ) | 0.140133230873501 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 57.3
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 11.8
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.4
Wood et al 2018 ( South Africa ) 0.3071 [-0.1311; 0.7452] 5.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.3
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.6
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.6
%W(random)
Subramanian et al 2014 ( Bangladesh ) 40.5
Azad et al 2015 ( Canada ) 15.7
Bender et al 2016 ( Haiti ) 4.0
Wood et al 2018 ( South Africa ) 8.9
Pannaraj et al 2017 ( USA(CA_FL) ) 17.2
Sordillo et al 2017 ( USA(CA_MA_MO) ) 11.0
Thompson et al 2015 ( USA(NC) ) 2.7
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.3153 [0.2088; 0.4219] 5.80 < 0.0001
Random effects model 0.3359 [0.1959; 0.4759] 4.70 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0074; H = 1.12 [1.00; 1.67]; I^2 = 20.9% [0.0%; 64.3%]
Test of heterogeneity:
Q d.f. p-value
7.59 6 0.2700
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2018 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
Show the results of Shannon indexes only.
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 58.8
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.1
Wood et al 2018 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.1
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.8
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 45.8
Azad et al 2015 ( Canada ) 15.5
Wood et al 2018 ( South Africa ) 8.5
Pannaraj et al 2017 ( USA(CA_FL) ) 17.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 10.6
Thompson et al 2015 ( USA(NC) ) 2.5
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.3261 [0.2183; 0.4340] 5.93 < 0.0001
Random effects model 0.3483 [0.2145; 0.4821] 5.10 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0050; H = 1.10 [1.00; 1.61]; I^2 = 16.9% [0.0%; 61.6%]
Test of heterogeneity:
Q d.f. p-value
6.02 5 0.3047
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Wood et al 2018 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 58.3
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.0
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.5
Wood et al 2018 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.5
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 36.5
Azad et al 2015 ( Canada ) 17.2
Bender et al 2016 ( Haiti ) 4.9
Wood et al 2018 ( South Africa ) 10.3
Pannaraj et al 2017 ( USA(CA_FL) ) 18.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 12.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.3156 [0.2082; 0.4230] 5.76 < 0.0001
Random effects model 0.3427 [0.1851; 0.5004] 4.26 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0126; H = 1.23 [1.00; 1.94]; I^2 = 34.1% [0.0%; 73.5%]
Test of heterogeneity:
Q d.f. p-value
7.58 5 0.1807
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2018 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 62.0
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.8
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.7
Wood et al 2018 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.4
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 14.4
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.8
%W(random)
Subramanian et al 2014 ( Bangladesh ) 62.0
Azad et al 2015 ( Canada ) 12.8
Bender et al 2016 ( Haiti ) 2.7
Wood et al 2018 ( South Africa ) 6.4
Pannaraj et al 2017 ( USA(CA_FL) ) 14.4
Thompson et al 2015 ( USA(NC) ) 1.8
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.2780 [0.1672; 0.3889] 4.92 < 0.0001
Random effects model 0.2780 [0.1672; 0.3889] 4.92 < 0.0001
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.21]; I^2 = 0.0% [0.0%; 32.0%]
Test of heterogeneity:
Q d.f. p-value
1.87 5 0.8674
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2018 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
Show results of Shannon index only.
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.1424 [-0.0984; 0.3832] 40.8
Bender et al 2016 (Haiti) -0.2018 [-0.9752; 0.5715] 4.0
Pannaraj et al 2017 (USA(CA_FL)) 0.3734 [ 0.1294; 0.6174] 39.7
Sordillo et al 2017 (USA(CA_MA_MO)) 0.4321 [ 0.0420; 0.8223] 15.5
%W(random)
Azad et al 2015 (Canada) 38.3
Bender et al 2016 (Haiti) 5.4
Pannaraj et al 2017 (USA(CA_FL)) 37.6
Sordillo et al 2017 (USA(CA_MA_MO)) 18.6
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.2656 [0.1118; 0.4194] 3.38 0.0007
Random effects model 0.2647 [0.0798; 0.4495] 2.81 0.0050
Quantifying heterogeneity:
tau^2 = 0.0081; H = 1.13 [1.00; 2.90]; I^2 = 22.3% [0.0%; 88.1%]
Test of heterogeneity:
Q d.f. p-value
3.86 3 0.2771
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.246532761397953 |
| Bender et al 2016 (Haiti) | 0.608996225108868 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.00270151112577258 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.0299341350698865 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.4873 [ 0.0230; 0.9515] 40.3
Pannaraj et al 2017 (USA(CA_FL)) -0.0737 [-0.5869; 0.4395] 33.0
Sordillo et al 2017 (USA(CA_MA_MO)) 1.0833 [ 0.5127; 1.6540] 26.7
%W(random)
Azad et al 2015 (Canada) 34.9
Pannaraj et al 2017 (USA(CA_FL)) 33.4
Sordillo et al 2017 (USA(CA_MA_MO)) 31.7
Number of studies combined: k = 3
RD 95%-CI z p-value
Fixed effect model 0.4612 [ 0.1665; 0.7560] 3.07 0.0022
Random effects model 0.4888 [-0.1327; 1.1103] 1.54 0.1232
Quantifying heterogeneity:
tau^2 = 0.2323; H = 2.09 [1.16; 3.77]; I^2 = 77.1% [25.6%; 93.0%]
Test of heterogeneity:
Q d.f. p-value
8.75 2 0.0126
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.0396622679428872 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.778417002121859 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.000198560001433614 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| shannon | 0.3359260 | 0.0714283 | 0.1959290 | 0.4759229 | 4.702980 | 0.0000026 | 0.0000103 |
| observed_species | 0.2908894 | 0.0946918 | 0.1052969 | 0.4764819 | 3.071960 | 0.0021266 | 0.0029552 |
| pd_whole_tree | 0.1909514 | 0.0624970 | 0.0684595 | 0.3134432 | 3.055369 | 0.0022478 | 0.0029552 |
| chao1 | 0.2994547 | 0.1007464 | 0.1019953 | 0.4969141 | 2.972360 | 0.0029552 | 0.0029552 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0550 [-0.0189; 0.1289] 65.2
Azad et al 2015 ( Canada ) 0.5725 [ 0.3986; 0.7464] 11.8
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2018 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1302 [-0.0599; 0.3202] 9.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.4245 [ 0.2553; 0.5937] 12.4
Thompson et al 2015 ( USA(NC) ) 0.4233 [-0.2687; 1.1153] 0.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 24.7
Azad et al 2015 ( Canada ) 22.4
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2018 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 21.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 22.6
Thompson et al 2015 ( USA(NC) ) 8.3
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.1720 [0.1123; 0.2316] 5.65 < 0.0001
Random effects model 0.3016 [0.0580; 0.5451] 2.43 0.0152
Quantifying heterogeneity:
tau^2 = 0.0610; H = 3.13 [2.19; 4.49]; I^2 = 89.8% [79.1%; 95.0%]
Test of heterogeneity:
Q d.f. p-value
39.26 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.144460866036347 |
| Azad et al 2015 ( Canada ) | 1.0991009354299e-10 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2018 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.179455833167877 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 8.77670396356771e-07 |
| Thompson et al 2015 ( USA(NC) ) | 0.230600549600578 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0603 [-0.0124; 0.1329] 63.5
Azad et al 2015 ( Canada ) 0.5895 [ 0.4168; 0.7623] 11.2
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2018 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1163 [-0.0479; 0.2806] 12.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.4610 [ 0.2928; 0.6291] 11.9
Thompson et al 2015 ( USA(NC) ) 0.3661 [-0.2275; 0.9598] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 24.1
Azad et al 2015 ( Canada ) 21.9
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2018 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 22.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 22.0
Thompson et al 2015 ( USA(NC) ) 10.0
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.1772 [0.1192; 0.2351] 6.00 < 0.0001
Random effects model 0.3070 [0.0641; 0.5500] 2.48 0.0133
Quantifying heterogeneity:
tau^2 = 0.0625; H = 3.30 [2.33; 4.69]; I^2 = 90.8% [81.6%; 95.4%]
Test of heterogeneity:
Q d.f. p-value
43.68 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.104033167825551 |
| Azad et al 2015 ( Canada ) | 2.26960893212611e-11 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2018 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.165000455562882 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 7.73447284594136e-08 |
| Thompson et al 2015 ( USA(NC) ) | 0.226684364502839 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0646 [-0.0047; 0.1338] 72.9
Azad et al 2015 ( Canada ) 0.5311 [ 0.3540; 0.7082] 11.2
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2018 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2032 [ 0.0523; 0.3541] 15.4
Thompson et al 2015 ( USA(NC) ) 0.8566 [ 0.0509; 1.6623] 0.5
%W(random)
Subramanian et al 2014 ( Bangladesh ) 32.9
Azad et al 2015 ( Canada ) 29.1
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2018 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 30.2
Thompson et al 2015 ( USA(NC) ) 7.8
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.1422 [0.0830; 0.2013] 4.71 < 0.0001
Random effects model 0.3037 [0.0475; 0.5598] 2.32 0.0202
Quantifying heterogeneity:
tau^2 = 0.0506; H = 3.00 [1.97; 4.57]; I^2 = 88.9% [74.2%; 95.2%]
Test of heterogeneity:
Q d.f. p-value
26.99 3 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0676383461236607 |
| Azad et al 2015 ( Canada ) | 4.17049539317814e-09 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2018 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.00831447939658577 |
| Thompson et al 2015 ( USA(NC) ) | 0.0371791605971582 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2131 [ 0.0843; 0.3420] 39.0
Azad et al 2015 ( Canada ) 0.5872 [ 0.4153; 0.7590] 21.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2570 [ 0.0375; 0.4765] 13.5
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.5660 [ 0.4038; 0.7282] 24.6
Thompson et al 2015 ( USA(NC) ) -0.0180 [-0.8408; 0.8049] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 25.8
Azad et al 2015 ( Canada ) 23.8
Pannaraj et al 2017 ( USA(CA_FL) ) 21.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 24.2
Thompson et al 2015 ( USA(NC) ) 4.8
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.3858 [0.3053; 0.4663] 9.39 < 0.0001
Random effects model 0.3857 [0.1872; 0.5843] 3.81 0.0001
Quantifying heterogeneity:
tau^2 = 0.0355; H = 2.19 [1.42; 3.37]; I^2 = 79.1% [50.4%; 91.2%]
Test of heterogeneity:
Q d.f. p-value
19.16 4 0.0007
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.00119013497616748 |
| Azad et al 2015 ( Canada ) | 2.14964602978342e-11 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0217486284946625 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 7.9318409863511e-12 |
| Thompson et al 2015 ( USA(NC) ) | 0.965887658685873 |
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| shannon | 0.3857475 | 0.1012964 | 0.1872101 | 0.5842849 | 3.808105 | 0.0001400 | 0.0005601 |
| observed_species | 0.3070476 | 0.1239712 | 0.0640686 | 0.5500267 | 2.476766 | 0.0132579 | 0.0201585 |
| pd_whole_tree | 0.3036608 | 0.1306976 | 0.0474982 | 0.5598233 | 2.323384 | 0.0201585 | 0.0201585 |
| chao1 | 0.3015700 | 0.1242513 | 0.0580420 | 0.5450980 | 2.427098 | 0.0152201 | 0.0201585 |
Results of 7 studies.
For samples <= 6 months old only in all studies (note for USA(NC) study: GAMLSS BEZI with random subject effect could not run on very small sample size=> did not include subject random effect). Results of random meta-analysis models for taxa available in at least >50% of studies based on adjusted estimates and standard errors from GAMLSS models with zero-inflated beta family adjusted for infant age at sample collection.
GAMLSS models with zero-inflated beta family
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.25 | 0.0684909 | 0.11 | 0.38 | 3.616776 | 3e-04 | 0.0018 |
| k__bacteria.p__bacteroidetes | 0.21 | 0.0756683 | 0.06 | 0.36 | 2.748422 | 6e-03 | 0.0180 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.30 | 0.0904382 | 0.12 | 0.48 | 3.334046 | 0.0009 | 0.0106 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.21 | 0.0757620 | 0.06 | 0.36 | 2.772512 | 0.0056 | 0.0369 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.20 | 0.0896354 | 0.02 | 0.38 | 2.236847 | 0.0253 | 0.1170 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.23 | 0.0856673 | 0.06 | 0.40 | 2.698284 | 0.0070 | 0.0757 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.21 | 0.0807013 | 0.05 | 0.37 | 2.611789 | 0.0090 | 0.0856 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.20 | 0.0896354 | 0.02 | 0.38 | 2.236847 | 0.0253 | 0.1748 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.17 | 0.0841374 | 0.00 | 0.33 | 1.963771 | 0.0496 | 0.3087 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.39 | 0.1237182 | 0.15 | 0.64 | 3.173387 | 0.0015 | 0.0561 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.40 | 0.1416041 | 0.12 | 0.68 | 2.825361 | 0.0047 | 0.1115 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.21 | 0.0807013 | 0.05 | 0.37 | 2.611789 | 0.0090 | 0.1220 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.35 | 0.1505929 | 0.05 | 0.64 | 2.293839 | 0.0218 | 0.2513 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.21 | 0.1033136 | 0.01 | 0.42 | 2.068028 | 0.0386 | 0.3598 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.25 | 0.0691970 | 0.11 | 0.38 | 3.568106 | 0.0004 | 0.0025 |
| k__bacteria.p__bacteroidetes | 0.19 | 0.0763734 | 0.04 | 0.34 | 2.530586 | 0.0114 | 0.0399 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.28 | 0.0889258 | 0.11 | 0.46 | 3.170900 | 0.0015 | 0.0233 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.20 | 0.0764693 | 0.05 | 0.35 | 2.554669 | 0.0106 | 0.0873 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.20 | 0.0908867 | 0.02 | 0.38 | 2.190489 | 0.0285 | 0.1638 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.19 | 0.0815355 | 0.03 | 0.35 | 2.388972 | 0.0169 | 0.2092 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.22 | 0.0940439 | 0.04 | 0.41 | 2.373553 | 0.0176 | 0.2092 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.20 | 0.0908867 | 0.02 | 0.38 | 2.190489 | 0.0285 | 0.2460 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.40 | 0.1275892 | 0.15 | 0.65 | 3.111909 | 0.0019 | 0.0888 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.40 | 0.1416041 | 0.12 | 0.68 | 2.825361 | 0.0047 | 0.1804 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.24 | 0.0943469 | 0.06 | 0.43 | 2.570734 | 0.0101 | 0.2417 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.19 | 0.0815355 | 0.03 | 0.35 | 2.388972 | 0.0169 | 0.2804 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.35 | 0.1505929 | 0.05 | 0.64 | 2.293839 | 0.0218 | 0.3203 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.26 | 0.0699441 | 0.12 | 0.40 | 3.696729 | 0.0002 | 0.0013 |
| k__bacteria.p__bacteroidetes | 0.21 | 0.0769990 | 0.06 | 0.36 | 2.776286 | 0.0055 | 0.0165 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.32 | 0.0708228 | 0.18 | 0.46 | 4.515471 | 0.0000 | 0.0001 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.22 | 0.0770481 | 0.07 | 0.37 | 2.857121 | 0.0043 | 0.0325 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.18 | 0.0915095 | 0.00 | 0.36 | 2.010465 | 0.0444 | 0.2108 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.21 | 0.0822865 | 0.04 | 0.37 | 2.504798 | 0.0123 | 0.1348 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.21 | 0.0969374 | 0.02 | 0.40 | 2.126103 | 0.0335 | 0.2947 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.18 | 0.0915095 | 0.00 | 0.36 | 2.010465 | 0.0444 | 0.2947 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.17 | 0.0868412 | 0.00 | 0.34 | 1.996101 | 0.0459 | 0.2947 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.45 | 0.1519683 | 0.15 | 0.75 | 2.975441 | 0.0029 | 0.1063 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.36 | 0.1297330 | 0.11 | 0.61 | 2.770714 | 0.0056 | 0.1063 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.21 | 0.0822865 | 0.04 | 0.37 | 2.504798 | 0.0123 | 0.1862 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.36 | 0.1521514 | 0.06 | 0.65 | 2.338328 | 0.0194 | 0.2677 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.52 | 0.2401244 | 0.05 | 0.99 | 2.165979 | 0.0303 | 0.3840 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.53 | 0.2586130 | 0.03 | 1.04 | 2.066443 | 0.0388 | 0.3878 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes | 0.23 | 0.0810268 | 0.07 | 0.39 | 2.854058 | 0.0043 | 0.0251 |
| k__bacteria.p__firmicutes | 0.20 | 0.0745996 | 0.05 | 0.35 | 2.689210 | 0.0072 | 0.0251 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.23 | 0.0811408 | 0.07 | 0.39 | 2.880970 | 0.0040 | 0.0549 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.30 | 0.1099207 | 0.08 | 0.51 | 2.700967 | 0.0069 | 0.0549 |
| k__bacteria.p__actinobacteria.c__actinobacteria.o__actinomycetales | -0.16 | 0.0644216 | -0.28 | -0.03 | -2.418256 | 0.0156 | 0.1025 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.21 | 0.0993562 | 0.02 | 0.41 | 2.130727 | 0.0331 | 0.1692 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.21 | 0.1040509 | -0.41 | -0.01 | -2.026511 | 0.0427 | 0.1965 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.30 | 0.0741081 | 0.15 | 0.44 | 4.042869 | 0.0001 | 0.0050 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.24 | 0.0870795 | 0.07 | 0.41 | 2.727563 | 0.0064 | 0.0851 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.21 | 0.0993562 | 0.02 | 0.41 | 2.130727 | 0.0331 | 0.2621 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 2.06 | 0.5761745 | 0.93 | 3.19 | 3.582354 | 0.0003 | 0.0306 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.41 | 0.1362642 | 0.14 | 0.68 | 3.023725 | 0.0025 | 0.1074 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.45 | 0.1618768 | 0.14 | 0.77 | 2.799657 | 0.0051 | 0.1074 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.24 | 0.0870795 | 0.07 | 0.41 | 2.727563 | 0.0064 | 0.1074 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.26 | 0.1085724 | 0.05 | 0.47 | 2.404864 | 0.0162 | 0.2080 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.35 | 0.1505929 | 0.05 | 0.64 | 2.293839 | 0.0218 | 0.2616 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.55 | 0.2571987 | 0.04 | 1.05 | 2.126889 | 0.0334 | 0.3167 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria | -0.31 | 0.1017253 | -0.51 | -0.11 | -3.017517 | 0.0025 | 0.0178 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales | -0.30 | 0.1074593 | -0.51 | -0.09 | -2.782951 | 0.0054 | 0.1158 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.28 | 0.1232153 | 0.04 | 0.52 | 2.294944 | 0.0217 | 0.2337 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.33 | 0.1174047 | -0.56 | -0.10 | -2.833865 | 0.0046 | 0.1157 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | -0.30 | 0.1074593 | -0.51 | -0.09 | -2.782951 | 0.0054 | 0.1157 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.30 | 0.1105580 | 0.08 | 0.52 | 2.728721 | 0.0064 | 0.1157 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae | 0.80 | 0.3139899 | 0.19 | 1.42 | 2.562377 | 0.0104 | 0.1577 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.28 | 0.1232153 | 0.04 | 0.52 | 2.294944 | 0.0217 | 0.2198 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 3.37 | 0.4300060 | 2.53 | 4.21 | 7.833648 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.33 | 0.1174105 | -0.56 | -0.10 | -2.836711 | 0.0046 | 0.1176 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae.g__pseudoramibacter_eubacterium | 0.88 | 0.3157991 | 0.26 | 1.50 | 2.774622 | 0.0055 | 0.1176 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.32 | 0.1163513 | 0.09 | 0.55 | 2.733460 | 0.0063 | 0.1176 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.30 | 0.1105580 | 0.08 | 0.52 | 2.728721 | 0.0064 | 0.1176 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.54 | 0.2026827 | 0.14 | 0.94 | 2.656820 | 0.0079 | 0.1327 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | -0.29 | 0.1148106 | -0.51 | -0.06 | -2.493051 | 0.0127 | 0.1802 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.30 | 0.1238937 | 0.06 | 0.55 | 2.443764 | 0.0145 | 0.1921 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae.g__aggregatibacter | 0.57 | 0.2477375 | 0.09 | 1.06 | 2.309983 | 0.0209 | 0.2234 |
| k__bacteria.p__firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__lactococcus | 0.58 | 0.2676966 | 0.06 | 1.11 | 2.179940 | 0.0293 | 0.2849 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | 0.36 | 0.1848815 | 0.00 | 0.73 | 1.968416 | 0.0490 | 0.4534 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria | -0.72 | 0.1708821 | -1.05 | -0.38 | -4.211478 | 0 | 2e-04 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales | -0.58 | 0.2324176 | -1.03 | -0.12 | -2.493087 | 0.0127 | 0.1562 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | -0.58 | 0.2324176 | -1.03 | -0.12 | -2.493087 | 0.0127 | 0.2596 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__proteus | -0.26 | 0.0008395 | -0.26 | -0.26 | -307.189026 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__ruminococcaceae.g__anaerotruncus | -2.92 | 0.7060795 | -4.31 | -1.54 | -4.141797 | 0.0000 | 0.0019 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__phascolarctobacterium | -1.88 | 0.8567398 | -3.56 | -0.20 | -2.199114 | 0.0279 | 0.6490 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | -0.52 | 0.2608359 | -1.03 | -0.01 | -2.003505 | 0.0451 | 0.9154 |
Significant (pooled p<0.05) only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.29 | 0.0810164 | 0.13 | 0.45 | 3.568494 | 0.0004 | 0.0022 |
| k__bacteria.p__verrucomicrobia | 0.19 | 0.0798894 | 0.03 | 0.35 | 2.381818 | 0.0172 | 0.0517 |
| k__bacteria.p__bacteroidetes | 0.22 | 0.0979174 | 0.02 | 0.41 | 2.201999 | 0.0277 | 0.0553 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.39 | 0.0632438 | 0.27 | 0.52 | 6.205840 | 0.0000 | 0.0000 |
| k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales | 0.32 | 0.0545196 | 0.21 | 0.42 | 5.793673 | 0.0000 | 0.0000 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales | -0.22 | 0.0645356 | -0.34 | -0.09 | -3.376832 | 0.0007 | 0.0045 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.17 | 0.0523488 | -0.28 | -0.07 | -3.307732 | 0.0009 | 0.0050 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales | 0.19 | 0.0798894 | 0.03 | 0.35 | 2.381865 | 0.0172 | 0.0637 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.23 | 0.1084234 | 0.02 | 0.44 | 2.121104 | 0.0339 | 0.0965 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.20 | 0.0958110 | 0.01 | 0.39 | 2.062503 | 0.0392 | 0.0966 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | 0.32 | 0.0545196 | 0.21 | 0.42 | 5.793673 | 0.0000 | 0.0000 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae | -0.22 | 0.0645356 | -0.34 | -0.09 | -3.376832 | 0.0007 | 0.0070 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.18 | 0.0598847 | -0.30 | -0.07 | -3.074603 | 0.0021 | 0.0160 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae | 0.19 | 0.0716934 | 0.05 | 0.33 | 2.637485 | 0.0084 | 0.0577 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales.f__verrucomicrobiaceae | 0.19 | 0.0798894 | 0.03 | 0.35 | 2.381865 | 0.0172 | 0.0873 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__ruminococcaceae | 0.20 | 0.0874835 | 0.03 | 0.38 | 2.337166 | 0.0194 | 0.0923 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.14 | 0.0667077 | 0.01 | 0.27 | 2.127078 | 0.0334 | 0.1234 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae | 0.34 | 0.1598501 | 0.03 | 0.65 | 2.118964 | 0.0341 | 0.1234 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.20 | 0.0958110 | 0.01 | 0.39 | 2.062503 | 0.0392 | 0.1240 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.33 | 0.0063390 | 0.32 | 0.34 | 52.048471 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | 0.38 | 0.0668433 | 0.25 | 0.51 | 5.708296 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.38 | 0.0787618 | 0.23 | 0.53 | 4.829656 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.34 | 0.0781848 | 0.18 | 0.49 | 4.309681 | 0.0000 | 0.0003 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae.g__haemophilus | -0.23 | 0.0652393 | -0.36 | -0.10 | -3.495496 | 0.0005 | 0.0064 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.18 | 0.0594315 | -0.30 | -0.07 | -3.078824 | 0.0021 | 0.0196 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales.f__verrucomicrobiaceae.g__akkermansia | 0.19 | 0.0798897 | 0.03 | 0.35 | 2.387877 | 0.0169 | 0.1167 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae.g__ | 0.29 | 0.1410017 | 0.01 | 0.57 | 2.064129 | 0.0390 | 0.1823 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.05 | 0.0172713 | -0.08 | -0.01 | -2.770421 | 0.0056 | 0.1417 |
| Genetic.Information.Processing..Transcription | 0.02 | 0.0059866 | 0.00 | 0.03 | 2.666664 | 0.0077 | 0.1417 |
| Metabolism..Carbohydrate.Metabolism | 0.01 | 0.0063844 | 0.00 | 0.03 | 2.183138 | 0.0290 | 0.3580 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.08 | 0.0153155 | 0.05 | 0.11 | 5.095314 | 0.0000 | 0.0001 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.06 | 0.0148455 | -0.09 | -0.03 | -4.278043 | 0.0000 | 0.0021 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.09 | 0.0243173 | -0.14 | -0.04 | -3.669960 | 0.0002 | 0.0180 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.06 | 0.0187795 | 0.03 | 0.10 | 3.380198 | 0.0007 | 0.0380 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.04 | 0.0129610 | 0.02 | 0.07 | 3.335177 | 0.0009 | 0.0380 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.03 | 0.0089990 | -0.05 | -0.01 | -3.276602 | 0.0011 | 0.0390 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.08 | 0.0244139 | 0.03 | 0.13 | 3.197788 | 0.0014 | 0.0441 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.04 | 0.0119244 | 0.01 | 0.06 | 3.070645 | 0.0021 | 0.0595 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | 0.0242623 | -0.12 | -0.02 | -2.871463 | 0.0041 | 0.1012 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.12 | 0.0415301 | -0.20 | -0.04 | -2.817180 | 0.0048 | 0.1080 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.01 | 0.0053033 | 0.00 | 0.03 | 2.758214 | 0.0058 | 0.1178 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.04 | 0.0176901 | -0.08 | -0.01 | -2.498851 | 0.0125 | 0.2194 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.03 | 0.0128413 | 0.01 | 0.06 | 2.485508 | 0.0129 | 0.2194 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.03 | 0.0131930 | 0.01 | 0.06 | 2.463122 | 0.0138 | 0.2194 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.01 | 0.0049931 | -0.02 | 0.00 | -2.308193 | 0.0210 | 0.3120 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.03 | 0.0143473 | -0.06 | 0.00 | -2.218663 | 0.0265 | 0.3293 |
| Unclassified..Cellular.Processes.and.Signaling..Inorganic.ion.transport.and.metabolism | -0.07 | 0.0338473 | -0.14 | -0.01 | -2.211755 | 0.0270 | 0.3293 |
| Organismal.Systems..Endocrine.System..Insulin.signaling.pathway | 0.06 | 0.0270235 | 0.01 | 0.11 | 2.188835 | 0.0286 | 0.3293 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.03 | 0.0134249 | 0.00 | 0.06 | 2.148825 | 0.0316 | 0.3293 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.02 | 0.0099554 | 0.00 | 0.04 | 2.144209 | 0.0320 | 0.3293 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.10 | 0.0469254 | -0.19 | -0.01 | -2.136785 | 0.0326 | 0.3293 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Toluene.degradation | -0.07 | 0.0334904 | -0.14 | -0.01 | -2.123440 | 0.0337 | 0.3293 |
| Metabolism..Lipid.Metabolism..Glycerolipid.metabolism | 0.03 | 0.0164356 | 0.00 | 0.07 | 2.120529 | 0.0340 | 0.3293 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Glycosphingolipid.biosynthesis…globo.series | 0.08 | 0.0401464 | 0.00 | 0.16 | 1.996258 | 0.0459 | 0.4265 |
Nice plot all pathways
Nice plot significant pathways only (pooled p<0.05)
Nice plot multiple testing adjusted significant pathways only (adjusted pooled p<0.1)
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Organismal.Systems..Environmental.Adaptation | 0.05 | 0.0154241 | 0.02 | 0.08 | 3.171071 | 0.0015 | 0.0562 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.05 | 0.0176124 | -0.08 | -0.02 | -2.850687 | 0.0044 | 0.0807 |
| Genetic.Information.Processing..Transcription | 0.02 | 0.0063860 | 0.00 | 0.03 | 2.562214 | 0.0104 | 0.1283 |
| Metabolism..Carbohydrate.Metabolism | 0.01 | 0.0066286 | 0.00 | 0.03 | 1.976019 | 0.0482 | 0.4454 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.08 | 0.0162836 | 0.05 | 0.11 | 4.954756 | 0.0000 | 0.0002 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.07 | 0.0150202 | -0.09 | -0.04 | -4.332715 | 0.0000 | 0.0016 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.09 | 0.0230967 | -0.14 | -0.05 | -4.106429 | 0.0000 | 0.0030 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.07 | 0.0182025 | 0.03 | 0.10 | 3.626040 | 0.0003 | 0.0161 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.09 | 0.0249367 | 0.04 | 0.14 | 3.532866 | 0.0004 | 0.0184 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.04 | 0.0119845 | 0.02 | 0.06 | 3.311236 | 0.0009 | 0.0302 |
| Organismal.Systems..Environmental.Adaptation..Plant.pathogen.interaction | 0.05 | 0.0139004 | 0.02 | 0.07 | 3.307211 | 0.0009 | 0.0302 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.04 | 0.0142889 | 0.02 | 0.07 | 3.104340 | 0.0019 | 0.0534 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.13 | 0.0422790 | -0.21 | -0.05 | -3.025693 | 0.0025 | 0.0617 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | 0.0243975 | -0.12 | -0.02 | -2.921727 | 0.0035 | 0.0780 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.03 | 0.0100993 | -0.05 | -0.01 | -2.887504 | 0.0039 | 0.0791 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Porphyrin.and.chlorophyll.metabolism | 0.06 | 0.0223847 | 0.02 | 0.11 | 2.798977 | 0.0051 | 0.0957 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.04 | 0.0131564 | 0.01 | 0.06 | 2.766949 | 0.0057 | 0.0975 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.04 | 0.0131936 | 0.01 | 0.06 | 2.676042 | 0.0074 | 0.1192 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.01 | 0.0057662 | 0.00 | 0.03 | 2.578692 | 0.0099 | 0.1481 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.04 | 0.0180359 | 0.01 | 0.08 | 2.458094 | 0.0140 | 0.1955 |
| Unclassified..Cellular.Processes.and.Signaling..Inorganic.ion.transport.and.metabolism | -0.09 | 0.0365552 | -0.16 | -0.01 | -2.365195 | 0.0180 | 0.2374 |
| Metabolism..Lipid.Metabolism..Glycerolipid.metabolism | 0.04 | 0.0163608 | 0.01 | 0.07 | 2.333573 | 0.0196 | 0.2441 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Toluene.degradation | -0.08 | 0.0346447 | -0.15 | -0.01 | -2.278094 | 0.0227 | 0.2625 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.11 | 0.0475573 | -0.20 | -0.01 | -2.266188 | 0.0234 | 0.2625 |
| Organismal.Systems..Endocrine.System..Insulin.signaling.pathway | 0.06 | 0.0275299 | 0.01 | 0.11 | 2.195500 | 0.0281 | 0.2935 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.01 | 0.0050446 | -0.02 | 0.00 | -2.185914 | 0.0288 | 0.2935 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.02 | 0.0100331 | 0.00 | 0.04 | 2.131286 | 0.0331 | 0.3220 |
| Metabolism..Amino.Acid.Metabolism..Glycine..serine.and.threonine.metabolism | -0.02 | 0.0072327 | -0.03 | 0.00 | -2.100542 | 0.0357 | 0.3249 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.03 | 0.0156436 | -0.06 | 0.00 | -2.088358 | 0.0368 | 0.3249 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Metabolism.of.xenobiotics.by.cytochrome.P450 | -0.10 | 0.0480715 | -0.19 | -0.01 | -2.067137 | 0.0387 | 0.3249 |
| Genetic.Information.Processing..Translation..RNA.transport | 0.06 | 0.0301254 | 0.00 | 0.12 | 2.062518 | 0.0392 | 0.3249 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Tetracycline.biosynthesis | 0.06 | 0.0281702 | 0.00 | 0.11 | 1.995717 | 0.0460 | 0.3526 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.10 | 0.0484326 | -0.19 | 0.00 | -1.990020 | 0.0466 | 0.3526 |
| Human.Diseases..Infectious.Diseases..Epithelial.cell.signaling.in.Helicobacter.pylori.infection | 0.05 | 0.0231344 | 0.00 | 0.09 | 1.981795 | 0.0475 | 0.3526 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.03 | 0.0143536 | 0.00 | 0.06 | 1.970387 | 0.0488 | 0.3526 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Glycan.Biosynthesis.and.Metabolism | 0.05 | 0.0115747 | 0.03 | 0.07 | 4.488883 | 0.0000 | 0.0003 |
| Genetic.Information.Processing..Transcription | 0.01 | 0.0051201 | 0.00 | 0.02 | 2.738122 | 0.0062 | 0.1143 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.05 | 0.0186842 | -0.08 | -0.01 | -2.483537 | 0.0130 | 0.1604 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.07 | 0.0140831 | 0.04 | 0.10 | 4.940987 | 0.0000 | 0.0002 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.06 | 0.0158836 | -0.09 | -0.03 | -3.738054 | 0.0002 | 0.0210 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.06 | 0.0186649 | -0.09 | -0.02 | -2.999156 | 0.0027 | 0.1536 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.09 | 0.0298817 | -0.15 | -0.03 | -2.997946 | 0.0027 | 0.1536 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Chaperones.and.folding.catalysts | 0.02 | 0.0083216 | 0.01 | 0.04 | 2.908510 | 0.0036 | 0.1595 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | 0.0246606 | -0.12 | -0.02 | -2.850372 | 0.0044 | 0.1595 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.05 | 0.0179837 | 0.01 | 0.09 | 2.793881 | 0.0052 | 0.1595 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.05 | 0.0163147 | 0.01 | 0.08 | 2.767657 | 0.0056 | 0.1595 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.07 | 0.0274480 | 0.02 | 0.13 | 2.613593 | 0.0090 | 0.2250 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.02 | 0.0095096 | -0.04 | -0.01 | -2.562315 | 0.0104 | 0.2313 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.05 | 0.0190681 | 0.01 | 0.09 | 2.517749 | 0.0118 | 0.2313 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.03 | 0.0133415 | 0.01 | 0.06 | 2.503966 | 0.0123 | 0.2313 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.04 | 0.0159839 | 0.01 | 0.07 | 2.384403 | 0.0171 | 0.2974 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Chloroalkane.and.chloroalkene.degradation | -0.04 | 0.0187390 | -0.08 | -0.01 | -2.350608 | 0.0187 | 0.3026 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.01 | 0.0059388 | 0.00 | 0.03 | 2.301070 | 0.0214 | 0.3222 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.10 | 0.0486254 | -0.20 | -0.01 | -2.153855 | 0.0313 | 0.4117 |
| Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.02 | 0.0084431 | 0.00 | 0.03 | 2.151673 | 0.0314 | 0.4117 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.03 | 0.0161602 | 0.00 | 0.07 | 2.134681 | 0.0328 | 0.4117 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.02 | 0.0107085 | 0.00 | 0.04 | 2.090228 | 0.0366 | 0.4353 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.10 | 0.0500534 | -0.20 | 0.00 | -2.026311 | 0.0427 | 0.4829 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.05 | 0.0174642 | -0.08 | -0.01 | -2.755588 | 0.0059 | 0.2168 |
| Genetic.Information.Processing..Transcription | 0.02 | 0.0066440 | 0.00 | 0.03 | 2.404959 | 0.0162 | 0.2992 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.07 | 0.0153469 | 0.04 | 0.10 | 4.874259 | 0.0000 | 0.0002 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.06 | 0.0150010 | -0.09 | -0.03 | -4.232451 | 0.0000 | 0.0026 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.09 | 0.0256901 | -0.14 | -0.04 | -3.356095 | 0.0008 | 0.0596 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.02 | 0.0054765 | 0.01 | 0.03 | 3.108958 | 0.0019 | 0.0875 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.06 | 0.0201180 | 0.02 | 0.10 | 3.073116 | 0.0021 | 0.0875 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.08 | 0.0248949 | 0.03 | 0.12 | 3.045504 | 0.0023 | 0.0875 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.03 | 0.0096273 | -0.05 | -0.01 | -2.972464 | 0.0030 | 0.0954 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.04 | 0.0143916 | 0.01 | 0.07 | 2.890399 | 0.0038 | 0.1005 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | 0.0245939 | -0.12 | -0.02 | -2.878143 | 0.0040 | 0.1005 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.03 | 0.0122911 | 0.01 | 0.06 | 2.762045 | 0.0057 | 0.1298 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.02 | 0.0101136 | 0.00 | 0.04 | 2.278763 | 0.0227 | 0.4660 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.01 | 0.0050162 | -0.02 | 0.00 | -2.211653 | 0.0270 | 0.5078 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.03 | 0.0142804 | 0.00 | 0.06 | 2.143191 | 0.0321 | 0.5078 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.10 | 0.0493909 | -0.20 | -0.01 | -2.107573 | 0.0351 | 0.5078 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.03 | 0.0125598 | 0.00 | 0.05 | 2.100403 | 0.0357 | 0.5078 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.10 | 0.0476250 | -0.19 | -0.01 | -2.097515 | 0.0359 | 0.5078 |
| Human.Diseases..Infectious.Diseases..Epithelial.cell.signaling.in.Helicobacter.pylori.infection | 0.05 | 0.0233794 | 0.00 | 0.09 | 2.039309 | 0.0414 | 0.5378 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.03 | 0.0154611 | -0.06 | 0.00 | -2.007333 | 0.0447 | 0.5378 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.03 | 0.0146735 | 0.00 | 0.06 | 1.970575 | 0.0488 | 0.5378 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Human.Diseases..Infectious.Diseases | -0.05 | 0.0139289 | -0.08 | -0.02 | -3.481839 | 0.0005 | 0.0189 |
| Human.Diseases..Neurodegenerative.Diseases | -0.08 | 0.0286090 | -0.14 | -0.03 | -2.936430 | 0.0033 | 0.0631 |
| Unclassified..Genetic.Information.Processing | -0.02 | 0.0083563 | -0.04 | 0.00 | -2.428091 | 0.0152 | 0.1607 |
| Environmental.Information.Processing..Signal.Transduction | -0.06 | 0.0231749 | -0.10 | -0.01 | -2.388463 | 0.0169 | 0.1607 |
| Metabolism..Metabolism.of.Other.Amino.Acids | -0.02 | 0.0076171 | -0.03 | 0.00 | -2.197602 | 0.0280 | 0.2126 |
Level 3 All
Significant only (pooled p<0.05)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.05 | 0.0092376 | 0.03 | 0.06 | 5.001030 | 0.0000 | 0.0001 |
| Metabolism..Carbohydrate.Metabolism..Propanoate.metabolism | -0.06 | 0.0134718 | -0.08 | -0.03 | -4.234055 | 0.0000 | 0.0026 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.10 | 0.0284718 | -0.16 | -0.04 | -3.488412 | 0.0005 | 0.0371 |
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.07 | 0.0219622 | 0.03 | 0.12 | 3.280725 | 0.0010 | 0.0593 |
| Unclassified..Cellular.Processes.and.Signaling..Sporulation | 0.27 | 0.0880246 | 0.10 | 0.44 | 3.057250 | 0.0022 | 0.0994 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.04 | 0.0132461 | 0.01 | 0.07 | 3.010830 | 0.0026 | 0.0994 |
| Metabolism..Enzyme.Families..Peptidases | 0.02 | 0.0072551 | 0.01 | 0.04 | 2.945901 | 0.0032 | 0.1053 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Pantothenate.and.CoA.biosynthesis | 0.02 | 0.0086275 | 0.01 | 0.04 | 2.657414 | 0.0079 | 0.2155 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.03 | 0.0132238 | 0.01 | 0.06 | 2.600904 | 0.0093 | 0.2155 |
| Metabolism..Carbohydrate.Metabolism..Butanoate.metabolism | -0.04 | 0.0152890 | -0.07 | -0.01 | -2.554916 | 0.0106 | 0.2155 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | -0.08 | 0.0298932 | -0.13 | -0.02 | -2.539817 | 0.0111 | 0.2155 |
| Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | -0.10 | 0.0410760 | -0.18 | -0.02 | -2.524773 | 0.0116 | 0.2155 |
| Metabolism..Amino.Acid.Metabolism..Lysine.degradation | -0.09 | 0.0377849 | -0.17 | -0.02 | -2.484310 | 0.0130 | 0.2155 |
| Environmental.Information.Processing..Membrane.Transport..Bacterial.secretion.system | -0.05 | 0.0193032 | -0.09 | -0.01 | -2.479047 | 0.0132 | 0.2155 |
| Unclassified..Genetic.Information.Processing..Replication..recombination.and.repair.proteins | -0.04 | 0.0181120 | -0.08 | -0.01 | -2.447159 | 0.0144 | 0.2198 |
| Environmental.Information.Processing..Signal.Transduction..Two.component.system | -0.06 | 0.0262962 | -0.11 | -0.01 | -2.320034 | 0.0203 | 0.2911 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.06 | 0.0266534 | 0.01 | 0.11 | 2.242983 | 0.0249 | 0.3300 |
| Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | 0.10 | 0.0437020 | 0.01 | 0.18 | 2.227115 | 0.0259 | 0.3300 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | -0.08 | 0.0386717 | -0.16 | -0.01 | -2.104844 | 0.0353 | 0.4255 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | -0.09 | 0.0434446 | -0.17 | 0.00 | -2.060227 | 0.0394 | 0.4327 |
| Metabolism..Energy.Metabolism..Methane.metabolism | 0.04 | 0.0173608 | 0.00 | 0.07 | 2.050251 | 0.0403 | 0.4327 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.03 | 0.0162180 | -0.06 | 0.00 | -2.025958 | 0.0428 | 0.4327 |
| Organismal.Systems..Endocrine.System..Insulin.signaling.pathway | 0.07 | 0.0351516 | 0.00 | 0.14 | 2.001871 | 0.0453 | 0.4327 |
| Environmental.Information.Processing..Membrane.Transport..Secretion.system | -0.05 | 0.0255435 | -0.10 | 0.00 | -1.992679 | 0.0463 | 0.4327 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.08 | 0.0405844 | 0.00 | 0.16 | 1.984209 | 0.0472 | 0.4327 |
Multiple testing adjusted Significant only (adjusted pooled p<0.1)
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Human.Diseases..Infectious.Diseases | -0.11 | 0.0258973 | -0.16 | -0.06 | -4.350903 | 0.0000 | 0.0005 |
| Environmental.Information.Processing..Signal.Transduction | -0.14 | 0.0372818 | -0.21 | -0.07 | -3.799334 | 0.0001 | 0.0028 |
| Unclassified..Poorly.Characterized | -0.18 | 0.0692044 | -0.32 | -0.04 | -2.605500 | 0.0092 | 0.0868 |
| Metabolism..Energy.Metabolism | 0.04 | 0.0147283 | 0.01 | 0.07 | 2.542920 | 0.0110 | 0.0868 |
| Human.Diseases..Neurodegenerative.Diseases | -0.14 | 0.0567741 | -0.25 | -0.03 | -2.529420 | 0.0114 | 0.0868 |
| Genetic.Information.Processing..Replication.and.Repair | 0.11 | 0.0472699 | 0.01 | 0.20 | 2.229488 | 0.0258 | 0.1311 |
| Metabolism..Nucleotide.Metabolism | 0.11 | 0.0510945 | 0.01 | 0.21 | 2.228820 | 0.0258 | 0.1311 |
| Metabolism..Amino.Acid.Metabolism | 0.03 | 0.0117885 | 0.00 | 0.05 | 2.174502 | 0.0297 | 0.1311 |
| Unclassified..Cellular.Processes.and.Signaling | -0.15 | 0.0711795 | -0.29 | -0.01 | -2.126222 | 0.0335 | 0.1311 |
| Metabolism..Carbohydrate.Metabolism | 0.03 | 0.0121865 | 0.00 | 0.05 | 2.114057 | 0.0345 | 0.1311 |
Level 3 All
Significant only (pooled p<0.05)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Amino.Acid.Metabolism..Lysine.degradation | -0.24 | 0.0589751 | -0.36 | -0.13 | -4.087199 | 0.0000 | 0.0052 |
| Environmental.Information.Processing..Membrane.Transport..Secretion.system | -0.17 | 0.0409038 | -0.25 | -0.09 | -4.077994 | 0.0000 | 0.0052 |
| Cellular.Processes..Cell.Motility..Cytoskeleton.proteins | 0.19 | 0.0501812 | 0.10 | 0.29 | 3.878754 | 0.0001 | 0.0080 |
| Environmental.Information.Processing..Signal.Transduction..Two.component.system | -0.16 | 0.0417345 | -0.24 | -0.07 | -3.745237 | 0.0002 | 0.0103 |
| Metabolism..Amino.Acid.Metabolism..Lysine.biosynthesis | 0.09 | 0.0261242 | 0.04 | 0.14 | 3.569470 | 0.0004 | 0.0148 |
| Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | -0.22 | 0.0612575 | -0.34 | -0.10 | -3.548736 | 0.0004 | 0.0148 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Thiamine.metabolism | 0.08 | 0.0227453 | 0.03 | 0.12 | 3.424647 | 0.0006 | 0.0201 |
| Metabolism..Lipid.Metabolism..Biosynthesis.of.unsaturated.fatty.acids | -0.16 | 0.0480023 | -0.25 | -0.07 | -3.329941 | 0.0009 | 0.0249 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.07 | 0.0212525 | 0.03 | 0.11 | 3.291685 | 0.0010 | 0.0253 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.15 | 0.0458870 | -0.24 | -0.06 | -3.247440 | 0.0012 | 0.0267 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Sulfur.relay.system | -0.14 | 0.0433387 | -0.22 | -0.05 | -3.165507 | 0.0015 | 0.0300 |
| Metabolism..Carbohydrate.Metabolism..Galactose.metabolism | 0.12 | 0.0364226 | 0.04 | 0.19 | 3.161364 | 0.0016 | 0.0300 |
| Genetic.Information.Processing..Replication.and.Repair..Mismatch.repair | 0.08 | 0.0269024 | 0.03 | 0.14 | 3.094126 | 0.0020 | 0.0348 |
| Metabolism..Enzyme.Families..Peptidases | 0.04 | 0.0120243 | 0.01 | 0.06 | 3.059696 | 0.0022 | 0.0362 |
| Unclassified..Cellular.Processes.and.Signaling..Inorganic.ion.transport.and.metabolism | -0.23 | 0.0753721 | -0.38 | -0.08 | -3.025179 | 0.0025 | 0.0379 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Phenylpropanoid.biosynthesis | 0.16 | 0.0543283 | 0.06 | 0.27 | 2.990393 | 0.0028 | 0.0379 |
| Genetic.Information.Processing..Replication.and.Repair..Nucleotide.excision.repair | 0.19 | 0.0633790 | 0.07 | 0.31 | 2.987096 | 0.0028 | 0.0379 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.09 | 0.0289330 | 0.03 | 0.14 | 2.954096 | 0.0031 | 0.0379 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.replication.proteins | 0.07 | 0.0241948 | 0.02 | 0.12 | 2.953335 | 0.0031 | 0.0379 |
| Unclassified..Cellular.Processes.and.Signaling..Sporulation | 0.43 | 0.1509691 | 0.13 | 0.72 | 2.820915 | 0.0048 | 0.0548 |
| Unclassified..Cellular.Processes.and.Signaling..Other.ion.coupled.transporters | -0.11 | 0.0387677 | -0.18 | -0.03 | -2.778113 | 0.0055 | 0.0596 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | -0.15 | 0.0536771 | -0.25 | -0.04 | -2.713844 | 0.0067 | 0.0667 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | -0.12 | 0.0442873 | -0.21 | -0.03 | -2.709852 | 0.0067 | 0.0667 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.05 | 0.0195297 | 0.01 | 0.09 | 2.697465 | 0.0070 | 0.0667 |
| Unclassified..Metabolism..Metabolism.of.cofactors.and.vitamins | -0.13 | 0.0498366 | -0.23 | -0.04 | -2.676021 | 0.0075 | 0.0682 |
| Human.Diseases..Infectious.Diseases..Vibrio.cholerae.pathogenic.cycle | -0.13 | 0.0476819 | -0.22 | -0.03 | -2.658069 | 0.0079 | 0.0692 |
| Metabolism..Nucleotide.Metabolism..Pyrimidine.metabolism | 0.11 | 0.0429456 | 0.03 | 0.19 | 2.571884 | 0.0101 | 0.0816 |
| Metabolism..Amino.Acid.Metabolism..Phenylalanine..tyrosine.and.tryptophan.biosynthesis | 0.08 | 0.0298059 | 0.02 | 0.13 | 2.545772 | 0.0109 | 0.0816 |
| Unclassified..Poorly.Characterized..Function.unknown | -0.16 | 0.0616904 | -0.28 | -0.04 | -2.543364 | 0.0110 | 0.0816 |
| Unclassified..Metabolism..Biosynthesis.and.biodegradation.of.secondary.metabolites | -0.22 | 0.0850259 | -0.38 | -0.05 | -2.538914 | 0.0111 | 0.0816 |
| Metabolism..Enzyme.Families..Protein.kinases | -0.13 | 0.0510231 | -0.23 | -0.03 | -2.534648 | 0.0113 | 0.0816 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..One.carbon.pool.by.folate | 0.14 | 0.0568953 | 0.03 | 0.26 | 2.530320 | 0.0114 | 0.0816 |
| Metabolism..Energy.Metabolism..Methane.metabolism | 0.06 | 0.0251859 | 0.01 | 0.11 | 2.516847 | 0.0118 | 0.0822 |
| Cellular.Processes..Cell.Growth.and.Death..Cell.cycle…Caulobacter | 0.21 | 0.0840125 | 0.04 | 0.37 | 2.462727 | 0.0138 | 0.0929 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.replication | 0.10 | 0.0391391 | 0.02 | 0.17 | 2.444083 | 0.0145 | 0.0950 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Ubiquinone.and.other.terpenoid.quinone.biosynthesis | -0.13 | 0.0541391 | -0.24 | -0.02 | -2.391946 | 0.0168 | 0.1066 |
| Human.Diseases..Infectious.Diseases..Pertussis | -0.35 | 0.1463292 | -0.63 | -0.06 | -2.363893 | 0.0181 | 0.1119 |
| Metabolism..Carbohydrate.Metabolism..Starch.and.sucrose.metabolism | 0.10 | 0.0416485 | 0.02 | 0.18 | 2.325456 | 0.0200 | 0.1187 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Polycyclic.aromatic.hydrocarbon.degradation | 0.17 | 0.0745087 | 0.03 | 0.32 | 2.319764 | 0.0204 | 0.1187 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Pantothenate.and.CoA.biosynthesis | 0.04 | 0.0172203 | 0.01 | 0.07 | 2.312943 | 0.0207 | 0.1187 |
| Unclassified..Cellular.Processes.and.Signaling..Electron.transfer.carriers | -0.32 | 0.1370671 | -0.58 | -0.05 | -2.299820 | 0.0215 | 0.1199 |
| Cellular.Processes..Cell.Motility..Bacterial.motility.proteins | -0.20 | 0.0868495 | -0.37 | -0.03 | -2.261725 | 0.0237 | 0.1293 |
| Metabolism..Amino.Acid.Metabolism..Amino.acid.related.enzymes | 0.10 | 0.0459318 | 0.01 | 0.19 | 2.240355 | 0.0251 | 0.1335 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Peptidoglycan.biosynthesis | 0.17 | 0.0742134 | 0.02 | 0.31 | 2.230095 | 0.0257 | 0.1337 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis.proteins | -0.49 | 0.2211418 | -0.92 | -0.06 | -2.222040 | 0.0263 | 0.1337 |
| Unclassified..Cellular.Processes.and.Signaling..Membrane.and.intracellular.structural.molecules | -0.32 | 0.1470898 | -0.61 | -0.04 | -2.209314 | 0.0272 | 0.1338 |
| Metabolism..Energy.Metabolism..Photosynthesis | 0.31 | 0.1402569 | 0.03 | 0.58 | 2.204900 | 0.0275 | 0.1338 |
| Metabolism..Energy.Metabolism..Photosynthesis.proteins | 0.29 | 0.1367362 | 0.02 | 0.56 | 2.138483 | 0.0325 | 0.1420 |
| Genetic.Information.Processing..Replication.and.Repair..Homologous.recombination | 0.15 | 0.0711988 | 0.01 | 0.29 | 2.136688 | 0.0326 | 0.1420 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Protein.export | 0.20 | 0.0937140 | 0.02 | 0.38 | 2.136099 | 0.0327 | 0.1420 |
| Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | 0.32 | 0.1483752 | 0.03 | 0.61 | 2.130141 | 0.0332 | 0.1420 |
| Genetic.Information.Processing..Translation..Translation.factors | 0.20 | 0.0932695 | 0.02 | 0.38 | 2.122070 | 0.0338 | 0.1420 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.repair.and.recombination.proteins | 0.14 | 0.0668713 | 0.01 | 0.27 | 2.117768 | 0.0342 | 0.1420 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Prenyltransferases | 0.07 | 0.0325922 | 0.01 | 0.13 | 2.114184 | 0.0345 | 0.1420 |
| Unclassified..Poorly.Characterized..General.function.prediction.only | -0.15 | 0.0699906 | -0.29 | -0.01 | -2.113968 | 0.0345 | 0.1420 |
| Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | -0.12 | 0.0558385 | -0.23 | -0.01 | -2.111638 | 0.0347 | 0.1420 |
| Metabolism..Metabolism.of.Other.Amino.Acids..beta.Alanine.metabolism | -0.15 | 0.0714335 | -0.29 | -0.01 | -2.044687 | 0.0409 | 0.1643 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | -0.18 | 0.0900308 | -0.36 | -0.01 | -2.035126 | 0.0418 | 0.1652 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.siderophore.group.nonribosomal.peptides | -0.28 | 0.1381849 | -0.55 | -0.01 | -2.017012 | 0.0437 | 0.1690 |
| Genetic.Information.Processing..Translation..Ribosome | 0.26 | 0.1303595 | 0.01 | 0.52 | 2.011413 | 0.0443 | 0.1690 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Toluene.degradation | -0.09 | 0.0471773 | -0.19 | 0.00 | -1.997887 | 0.0457 | 0.1717 |
| Genetic.Information.Processing..Replication.and.Repair..Chromosome | 0.03 | 0.0141358 | 0.00 | 0.06 | 1.988861 | 0.0467 | 0.1725 |
| Metabolism..Carbohydrate.Metabolism..Glyoxylate.and.dicarboxylate.metabolism | -0.10 | 0.0482937 | -0.19 | 0.00 | -1.971762 | 0.0486 | 0.1768 |
Multiple testing adjusted Significant only (adjusted pooled p<0.1)
All analyses are adjusted for age of infants or breastfeeding status at sample collection and accounting for repeated/longitudinal sample collection.
For Subramanian (Bangladesh) data only.
Change in taxa relative abundance in duration of exclusive bf >2months vs. <=2 months
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes | -0.25 | 0.0633103 | -3.872828 | 0.0001 | 0.0005 | -0.37 | -0.12 |
| actinobacteria | 0.23 | 0.0709545 | 3.196223 | 0.0015 | 0.0029 | 0.09 | 0.37 |
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales | -0.25 | 0.0652555 | -3.808244 | 0.0002 | 0.0007 | -0.38 | -0.12 |
| firmicutes.c__bacilli.o__lactobacillales | -0.27 | 0.0725448 | -3.729979 | 0.0002 | 0.0007 | -0.41 | -0.13 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales | 0.25 | 0.0712188 | 3.570704 | 0.0004 | 0.0009 | 0.11 | 0.39 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales | -0.15 | 0.0757899 | -2.010438 | 0.0448 | 0.0784 | -0.30 | 0.00 |
Grey
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__lactobacillaceae | -0.31 | 0.0757692 | -4.099792 | 0.0000 | 0.0006 | -0.46 | -0.16 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.25 | 0.0652555 | -3.808244 | 0.0002 | 0.0010 | -0.38 | -0.12 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | 0.25 | 0.0712188 | 3.570704 | 0.0004 | 0.0017 | 0.11 | 0.39 |
| bacteroidetes.c__bacteroidia.o__bacteroidales.f__prevotellaceae | -0.27 | 0.0800336 | -3.353959 | 0.0008 | 0.0027 | -0.43 | -0.11 |
| firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | -0.22 | 0.0799003 | -2.719980 | 0.0067 | 0.0174 | -0.37 | -0.06 |
| firmicutes.c__bacilli.o__lactobacillales.f__enterococcaceae | 0.19 | 0.0817407 | 2.344727 | 0.0193 | 0.0419 | 0.03 | 0.35 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | -0.15 | 0.0757899 | -2.010438 | 0.0448 | 0.0789 | -0.30 | 0.00 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae | -0.14 | 0.0722439 | -1.976243 | 0.0486 | 0.0789 | -0.28 | 0.00 |
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__lactobacillaceae.g__lactobacillus | -0.33 | 0.0755929 | -4.385561 | 0.0000 | 0.0003 | -0.48 | -0.18 |
| firmicutes.c__clostridia.oclostridiales.f.g__ | -0.34 | 0.0803138 | -4.190128 | 0.0000 | 0.0003 | -0.49 | -0.18 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | 0.25 | 0.0712187 | 3.570578 | 0.0004 | 0.0027 | 0.11 | 0.39 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__.ruminococcus. | -0.25 | 0.0741715 | -3.393195 | 0.0007 | 0.0035 | -0.40 | -0.11 |
| bacteroidetes.c__bacteroidia.o__bacteroidales.f__prevotellaceae.g__prevotella | -0.27 | 0.0800336 | -3.353932 | 0.0008 | 0.0035 | -0.43 | -0.11 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | -0.22 | 0.0720564 | -3.016054 | 0.0027 | 0.0093 | -0.36 | -0.08 |
| firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | -0.24 | 0.0847773 | -2.866116 | 0.0043 | 0.0129 | -0.41 | -0.08 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | -0.22 | 0.0791422 | -2.768889 | 0.0058 | 0.0152 | -0.37 | -0.06 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.17 | 0.0682455 | -2.504614 | 0.0125 | 0.0292 | -0.30 | -0.04 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__catenibacterium | -0.23 | 0.0955240 | -2.404645 | 0.0165 | 0.0346 | -0.42 | -0.04 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | -0.16 | 0.0722253 | -2.233574 | 0.0259 | 0.0494 | -0.30 | -0.02 |
| firmicutes.c__bacilli.o__lactobacillales.f__enterococcaceae.g__enterococcus | 0.18 | 0.0833351 | 2.161482 | 0.0310 | 0.0543 | 0.02 | 0.34 |
Subramania (Bangladesh) data only.
Only LME was used as GAMLSS has issues with small sample size (when stratifying). LME as showed above has lower power than GAMLSS in general.
In infants with duration of exclusive bf <=2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.77 | 0.1993835 | -3.869376 | 0.0001 | 0.0017 | -1.16 | -0.38 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.69 | 0.1960537 | -3.525664 | 0.0005 | 0.0031 | -1.08 | -0.31 |
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae | 0.53 | 0.1836007 | 2.865417 | 0.0044 | 0.0191 | 0.17 | 0.89 |
In infants with duration of exclusive bf >2 months
estimate se teststat pval pval.adjust ll ul ——— — ——— —– ———— — —
GAMLSS
In infants with duration of exclusive bf <=2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.77 | 0.1993838 | -3.869325 | 0.0001 | 0.0027 | -1.16 | -0.38 |
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__streptococcus | 0.52 | 0.1841506 | 2.847491 | 0.0046 | 0.0488 | 0.16 | 0.89 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.50 | 0.2105904 | -2.370786 | 0.0183 | 0.1237 | -0.91 | -0.09 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | -0.50 | 0.2188542 | -2.273476 | 0.0236 | 0.1237 | -0.93 | -0.07 |
In infants with duration of exclusive bf >2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.39 | 0.2285308 | 1.688668 | 0.0923 | 0.9809 | -0.06 | 0.83 |
In non-exclusive bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.34 | 0.1461708 | -2.353678 | 0.0189 | 0.2458 | -0.63 | -0.06 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.25 | 0.1516653 | -1.656799 | 0.0981 | 0.4727 | -0.55 | 0.05 |
In no bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae | 2.09 | 0.6246379 | 3.347308 | 0.0018 | 0.0228 | 0.87 | 3.32 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -1.84 | 0.7653211 | -2.404776 | 0.0208 | 0.1351 | -3.34 | -0.34 |
In bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.29 | 0.1480753 | -1.965286 | 0.0498 | 0.6547 | -0.58 | 0.00 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.25 | 0.1516657 | -1.656853 | 0.0981 | 0.6547 | -0.55 | 0.05 |
In non-bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__streptococcus | 2.09 | 0.6249206 | 3.337650 | 0.0018 | 0.0379 | 0.86 | 3.31 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -1.84 | 0.7653209 | -2.404758 | 0.0208 | 0.2182 | -3.34 | -0.34 |
With GAMM fit and 95%CI.
LME fit <=2 months
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 10.3788398 | 0.2835665 | 36.6010753 | 0.0000000 |
| dia.exbf2No.>2 months | -1.1507899 | 0.4879123 | -2.3585999 | 0.0186104 |
| dia.exbf2Yes.<=2 months | -1.1945958 | 0.4839537 | -2.4684094 | 0.0138028 |
| dia.exbf2Yes.>2 months | -0.5097696 | 0.8117265 | -0.6280066 | 0.5301988 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 5.032806 | 5.032806 | 251.05395 | 0 |
| s(age.sample):dia.exbf2No.>2 months | 4.191756 | 4.191756 | 149.07931 | 0 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 37.58735 | 0 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 49.79342 | 0 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 10.3788398 | 0.2843456 | 689 | 36.500798 | 0.0000000 |
| Xdia.exbf2No.>2 months | -1.1507899 | 0.4892527 | 689 | -2.352138 | 0.0189463 |
| Xdia.exbf2Yes.<=2 months | -1.1945958 | 0.4852832 | 689 | -2.461647 | 0.0140740 |
| Xdia.exbf2Yes.>2 months | -0.5097696 | 0.8139565 | 689 | -0.626286 | 0.5313348 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 1.8308388 | 1.3486999 | 689 | 1.357484 | 0.1750718 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 1.6657329 | 1.3242074 | 689 | 1.257909 | 0.2088507 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 3.4720580 | 0.5678815 | 689 | 6.114054 | 0.0000000 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 5.0913209 | 0.7234958 | 689 | 7.037112 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 3.7678265 | 0.3316981 | 11.359203 | 0.0000000 |
| age.sample | 0.6832422 | 0.0173814 | 39.308910 | 0.0000000 |
| month.exbf2>2 months | -1.2353814 | 0.5064509 | -2.439291 | 0.0147161 |
| diarrheaYes | -1.0072569 | 0.5024243 | -2.004793 | 0.0449851 |
| month.exbf2>2 months:diarrheaYes | 1.8143024 | 0.9006571 | 2.014421 | 0.0439654 |
With GAMM fit and 95%CI.
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 3.0665206 | 0.0823202 | 37.2511259 | 0.0000000 |
| dia.exbf2No.>2 months | -0.1567257 | 0.1292484 | -1.2125925 | 0.2255782 |
| dia.exbf2Yes.<=2 months | -0.5837970 | 0.1257959 | -4.6408273 | 0.0000039 |
| dia.exbf2Yes.>2 months | -0.0919724 | 0.1901039 | -0.4838004 | 0.6286357 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.000000 | 1.000000 | 511.09021 | 0.00e+00 |
| s(age.sample):dia.exbf2No.>2 months | 5.974811 | 5.974811 | 75.05942 | 0.00e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 15.96302 | 6.93e-05 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 43.95975 | 0.00e+00 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 3.0665206 | 0.0824874 | 935 | 37.175641 | 0.0000000 |
| Xdia.exbf2No.>2 months | -0.1567257 | 0.1295109 | 935 | -1.210135 | 0.2265328 |
| Xdia.exbf2Yes.<=2 months | -0.5837970 | 0.1260513 | 935 | -4.631425 | 0.0000041 |
| Xdia.exbf2Yes.>2 months | -0.0919724 | 0.1904900 | 935 | -0.482820 | 0.6293366 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 0.8428954 | 0.0373599 | 935 | 22.561490 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -0.7155803 | 0.5005884 | 935 | -1.429479 | 0.1532008 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 0.5554706 | 0.1393107 | 935 | 3.987278 | 0.0000720 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 0.9760833 | 0.1475164 | 935 | 6.616780 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 3.0665206 | 0.0823202 | 37.2511259 | 0.0000000 |
| dia.exbf2No.>2 months | -0.1567257 | 0.1292484 | -1.2125925 | 0.2255782 |
| dia.exbf2Yes.<=2 months | -0.5837970 | 0.1257959 | -4.6408273 | 0.0000039 |
| dia.exbf2Yes.>2 months | -0.0919724 | 0.1901039 | -0.4838004 | 0.6286357 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.000000 | 1.000000 | 511.09021 | 0.00e+00 |
| s(age.sample):dia.exbf2No.>2 months | 5.974811 | 5.974811 | 75.05942 | 0.00e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 15.96302 | 6.93e-05 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 43.95975 | 0.00e+00 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 3.0665206 | 0.0824874 | 935 | 37.175641 | 0.0000000 |
| Xdia.exbf2No.>2 months | -0.1567257 | 0.1295109 | 935 | -1.210135 | 0.2265328 |
| Xdia.exbf2Yes.<=2 months | -0.5837970 | 0.1260513 | 935 | -4.631425 | 0.0000041 |
| Xdia.exbf2Yes.>2 months | -0.0919724 | 0.1904900 | 935 | -0.482820 | 0.6293366 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 0.8428954 | 0.0373599 | 935 | 22.561490 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -0.7155803 | 0.5005884 | 935 | -1.429479 | 0.1532008 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 0.5554706 | 0.1393107 | 935 | 3.987278 | 0.0000720 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 0.9760833 | 0.1475164 | 935 | 6.616780 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 1.8029966 | 0.0917394 | 19.653450 | 0.0000000 |
| age.sample | 0.1228124 | 0.0040692 | 30.181133 | 0.0000000 |
| month.exbf2>2 months | -0.1604039 | 0.1316082 | -1.218798 | 0.2229207 |
| diarrheaYes | -0.5210706 | 0.1247534 | -4.176806 | 0.0000296 |
| month.exbf2>2 months:diarrheaYes | 0.5706337 | 0.1973949 | 2.890823 | 0.0038423 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 151.196675 | 8.778134 | 17.2242389 | 0.0000000 |
| dia.exbf2No.>2 months | 6.376610 | 13.831570 | 0.4610185 | 0.6448877 |
| dia.exbf2Yes.<=2 months | -32.741233 | 8.978024 | -3.6468195 | 0.0002795 |
| dia.exbf2Yes.>2 months | 8.288239 | 17.024836 | 0.4868322 | 0.6264862 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 2.241236 | 2.241236 | 186.022933 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.803475 | 4.803475 | 86.288380 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 9.841034 | 0.0017564 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 34.546738 | 0.0000000 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 151.196675 | 8.795958 | 935 | 17.1893366 | 0.0000000 |
| Xdia.exbf2No.>2 months | 6.376610 | 13.859654 | 935 | 0.4600843 | 0.6455627 |
| Xdia.exbf2Yes.<=2 months | -32.741233 | 8.996254 | 935 | -3.6394298 | 0.0002882 |
| Xdia.exbf2Yes.>2 months | 8.288239 | 17.059405 | 935 | 0.4858457 | 0.6271904 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 51.801469 | 8.730802 | 935 | 5.9331857 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -19.877541 | 26.849174 | 935 | -0.7403409 | 0.4592790 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 31.121465 | 9.940785 | 935 | 3.1306850 | 0.0017981 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 61.612841 | 10.503858 | 935 | 5.8657345 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 151.196675 | 8.778134 | 17.2242389 | 0.0000000 |
| dia.exbf2No.>2 months | 6.376610 | 13.831570 | 0.4610185 | 0.6448877 |
| dia.exbf2Yes.<=2 months | -32.741233 | 8.978024 | -3.6468195 | 0.0002795 |
| dia.exbf2Yes.>2 months | 8.288239 | 17.024836 | 0.4868322 | 0.6264862 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 2.241236 | 2.241236 | 186.022933 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.803475 | 4.803475 | 86.288380 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 9.841034 | 0.0017564 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 34.546738 | 0.0000000 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 151.196675 | 8.795958 | 935 | 17.1893366 | 0.0000000 |
| Xdia.exbf2No.>2 months | 6.376610 | 13.859654 | 935 | 0.4600843 | 0.6455627 |
| Xdia.exbf2Yes.<=2 months | -32.741233 | 8.996254 | 935 | -3.6394298 | 0.0002882 |
| Xdia.exbf2Yes.>2 months | 8.288239 | 17.059405 | 935 | 0.4858457 | 0.6271904 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 51.801469 | 8.730802 | 935 | 5.9331857 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -19.877541 | 26.849174 | 935 | -0.7403409 | 0.4592790 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 31.121465 | 9.940785 | 935 | 3.1306850 | 0.0017981 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 61.612841 | 10.503858 | 935 | 5.8657345 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 67.218370 | 9.3632479 | 7.1789587 | 0.0000000 |
| age.sample | 8.165080 | 0.2895546 | 28.1987576 | 0.0000000 |
| month.exbf2>2 months | 6.548791 | 14.1631117 | 0.4623836 | 0.6438062 |
| diarrheaYes | -27.156839 | 8.8730060 | -3.0606132 | 0.0022088 |
| month.exbf2>2 months:diarrheaYes | 28.115237 | 14.0092249 | 2.0069088 | 0.0447594 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.1473183 | 0.4242502 | 26.2753392 | 0.0000000 |
| dia.exbf2No.>2 months | 0.2157323 | 0.6676390 | 0.3231271 | 0.7466679 |
| dia.exbf2Yes.<=2 months | -2.4295713 | 0.5177632 | -4.6924371 | 0.0000031 |
| dia.exbf2Yes.>2 months | -0.1330212 | 0.8797770 | -0.1511987 | 0.8798500 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.00000 | 1.00000 | 651.06494 | 0.0e+00 |
| s(age.sample):dia.exbf2No.>2 months | 4.26171 | 4.26171 | 146.66378 | 0.0e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.00000 | 1.00000 | 20.80080 | 5.7e-06 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.00000 | 1.00000 | 48.09244 | 0.0e+00 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.1473183 | 0.4251117 | 935 | 26.2220945 | 0.0000000 |
| Xdia.exbf2No.>2 months | 0.2157323 | 0.6689947 | 935 | 0.3224723 | 0.7471670 |
| Xdia.exbf2Yes.<=2 months | -2.4295713 | 0.5188143 | 935 | -4.6829302 | 0.0000032 |
| Xdia.exbf2Yes.>2 months | -0.1330212 | 0.8815636 | 935 | -0.1508923 | 0.8800932 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 3.9257946 | 0.1541688 | 935 | 25.4642659 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 0.5241955 | 1.3248785 | 935 | 0.3956555 | 0.6924494 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 2.6094784 | 0.5733168 | 935 | 4.5515473 | 0.0000060 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 4.1958246 | 0.6062613 | 935 | 6.9208183 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.1473183 | 0.4242502 | 26.2753392 | 0.0000000 |
| dia.exbf2No.>2 months | 0.2157323 | 0.6676390 | 0.3231271 | 0.7466679 |
| dia.exbf2Yes.<=2 months | -2.4295713 | 0.5177632 | -4.6924371 | 0.0000031 |
| dia.exbf2Yes.>2 months | -0.1330212 | 0.8797770 | -0.1511987 | 0.8798500 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.00000 | 1.00000 | 651.06494 | 0.0e+00 |
| s(age.sample):dia.exbf2No.>2 months | 4.26171 | 4.26171 | 146.66378 | 0.0e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.00000 | 1.00000 | 20.80080 | 5.7e-06 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.00000 | 1.00000 | 48.09244 | 0.0e+00 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.1473183 | 0.4251117 | 935 | 26.2220945 | 0.0000000 |
| Xdia.exbf2No.>2 months | 0.2157323 | 0.6689947 | 935 | 0.3224723 | 0.7471670 |
| Xdia.exbf2Yes.<=2 months | -2.4295713 | 0.5188143 | 935 | -4.6829302 | 0.0000032 |
| Xdia.exbf2Yes.>2 months | -0.1330212 | 0.8815636 | 935 | -0.1508923 | 0.8800932 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 3.9257946 | 0.1541688 | 935 | 25.4642659 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 0.5241955 | 1.3248785 | 935 | 0.3956555 | 0.6924494 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 2.6094784 | 0.5733168 | 935 | 4.5515473 | 0.0000060 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 4.1958246 | 0.6062613 | 935 | 6.9208183 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 5.1010594 | 0.4591138 | 11.1106653 | 0.0000000 |
| age.sample | 0.5894225 | 0.0166254 | 35.4531752 | 0.0000000 |
| month.exbf2>2 months | 0.2033228 | 0.6822247 | 0.2980291 | 0.7656809 |
| diarrheaYes | -2.1261538 | 0.5095509 | -4.1726032 | 0.0000301 |
| month.exbf2>2 months:diarrheaYes | 1.7538795 | 0.8050786 | 2.1785195 | 0.0293674 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 367.19115 | 24.93875 | 14.7237215 | 0.0000000 |
| dia.exbf2No.>2 months | 16.36035 | 39.31689 | 0.4161151 | 0.6774169 |
| dia.exbf2Yes.<=2 months | -86.62794 | 23.43335 | -3.6967801 | 0.0002305 |
| dia.exbf2Yes.>2 months | 28.78746 | 47.08230 | 0.6114285 | 0.5410577 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.502023 | 1.502023 | 261.413376 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.677640 | 4.677640 | 76.504447 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 7.810505 | 0.0052936 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 29.909461 | 0.0000001 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 367.19115 | 24.98938 | 935 | 14.6938872 | 0.0000000 |
| Xdia.exbf2No.>2 months | 16.36035 | 39.39672 | 935 | 0.4152720 | 0.6780381 |
| Xdia.exbf2Yes.<=2 months | -86.62794 | 23.48093 | 935 | -3.6892894 | 0.0002379 |
| Xdia.exbf2Yes.>2 months | 28.78746 | 47.17789 | 935 | 0.6101897 | 0.5418844 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 134.05173 | 12.55943 | 935 | 10.6733923 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -43.96611 | 67.65832 | 935 | -0.6498257 | 0.5159644 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 72.36395 | 25.94559 | 935 | 2.7890649 | 0.0053934 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 149.59600 | 27.40922 | 935 | 5.4578722 | 0.0000001 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 367.19115 | 24.93875 | 14.7237215 | 0.0000000 |
| dia.exbf2No.>2 months | 16.36035 | 39.31689 | 0.4161151 | 0.6774169 |
| dia.exbf2Yes.<=2 months | -86.62794 | 23.43335 | -3.6967801 | 0.0002305 |
| dia.exbf2Yes.>2 months | 28.78746 | 47.08230 | 0.6114285 | 0.5410577 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.502023 | 1.502023 | 261.413376 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.677640 | 4.677640 | 76.504447 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 7.810505 | 0.0052936 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 29.909461 | 0.0000001 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 367.19115 | 24.98938 | 935 | 14.6938872 | 0.0000000 |
| Xdia.exbf2No.>2 months | 16.36035 | 39.39672 | 935 | 0.4152720 | 0.6780381 |
| Xdia.exbf2Yes.<=2 months | -86.62794 | 23.48093 | 935 | -3.6892894 | 0.0002379 |
| Xdia.exbf2Yes.>2 months | 28.78746 | 47.17789 | 935 | 0.6101897 | 0.5418844 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 134.05173 | 12.55943 | 935 | 10.6733923 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -43.96611 | 67.65832 | 935 | -0.6498257 | 0.5159644 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 72.36395 | 25.94559 | 935 | 2.7890649 | 0.0053934 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 149.59600 | 27.40922 | 935 | 5.4578722 | 0.0000001 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 161.48642 | 26.4705453 | 6.1006078 | 0.0000000 |
| age.sample | 20.00874 | 0.7538543 | 26.5419213 | 0.0000000 |
| month.exbf2>2 months | 16.28471 | 40.3235504 | 0.4038512 | 0.6863222 |
| diarrheaYes | -72.27871 | 23.0991493 | -3.1290636 | 0.0017536 |
| month.exbf2>2 months:diarrheaYes | 83.14805 | 36.4602574 | 2.2805118 | 0.0225774 |
| estimate.nebf | ll | ul | pval.nebf | index |
|---|---|---|---|---|
| 0.07 | -0.01 | 0.15 | 0.1028 | chao1 |
| 0.07 | -0.01 | 0.15 | 0.0990 | observed_species |
| 0.10 | 0.02 | 0.17 | 0.0136 | pd_whole_tree |
| 0.26 | 0.12 | 0.40 | 0.0003 | shannon |
| Estimate | Std. Error | df | t value | Pr(>|t|) | ll | ul | pop | |
|---|---|---|---|---|---|---|---|---|
| bfNon_exclusiveBF | 0.06 | 0.0598450 | 212.4315 | 0.9491631 | 0.3436 | -0.06 | 0.17 | Bangladesh |
| bfNo_BF | -0.08 | 0.1742787 | 249.9866 | -0.4524857 | 0.6513 | -0.42 | 0.26 | Bangladesh |
| age.sample | 0.09 | 0.0142278 | 236.2014 | 6.1990475 | 0.0000 | 0.06 | 0.12 | Bangladesh |
Phylum
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| proteobacteria | 0.37 | 0.1333990 | 2.808734 | 0.0053 | 0.0249 | 0.11 | 0.64 |
| actinobacteria | -0.37 | 0.1398279 | -2.658182 | 0.0083 | 0.0249 | -0.65 | -0.10 |
| firmicutes | 0.24 | 0.1195704 | 1.996826 | 0.0468 | 0.0749 | 0.00 | 0.47 |
| bacteroidetes | 0.26 | 0.1345960 | 1.968538 | 0.0499 | 0.0749 | 0.00 | 0.53 |
Order
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| proteobacteria.c__epsilonproteobacteria.o__campylobacterales | 0.92 | 0.2290519 | 4.021387 | 0.0001 | 0.0014 | 0.47 | 1.37 |
| proteobacteria.c__gammaproteobacteria.o__enterobacteriales | 0.38 | 0.1334088 | 2.833506 | 0.0049 | 0.0287 | 0.12 | 0.64 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales | -0.39 | 0.1410203 | -2.800917 | 0.0054 | 0.0287 | -0.67 | -0.12 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales | 0.28 | 0.1324409 | 2.119518 | 0.0349 | 0.1258 | 0.02 | 0.54 |
| firmicutes.c__bacilli.o__lactobacillales | 0.25 | 0.1209641 | 2.090957 | 0.0374 | 0.1258 | 0.02 | 0.49 |
Family
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae | -2.00 | 0.3808437 | -5.248336 | 0.0000 | 0.0000 | -2.75 | -1.25 |
| proteobacteria.c__epsilonproteobacteria.o__campylobacterales.f__campylobacteraceae | 0.96 | 0.2339144 | 4.104901 | 0.0001 | 0.0015 | 0.50 | 1.42 |
| proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | 0.38 | 0.1334088 | 2.833506 | 0.0049 | 0.0400 | 0.12 | 0.64 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.39 | 0.1410203 | -2.800917 | 0.0054 | 0.0400 | -0.67 | -0.12 |
| proteobacteria.c__gammaproteobacteria.o__aeromonadales.f__aeromonadaceae | 1.16 | 0.4709172 | 2.459184 | 0.0145 | 0.0887 | 0.24 | 2.08 |
| proteobacteria.c__betaproteobacteria.o__burkholderiales.f__alcaligenaceae | -1.07 | 0.4406262 | -2.438548 | 0.0153 | 0.0887 | -1.94 | -0.21 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | 0.28 | 0.1324409 | 2.119518 | 0.0349 | 0.1664 | 0.02 | 0.54 |
| bacteroidetes.c__bacteroidia.o__bacteroidales.f__porphyromonadaceae | 0.73 | 0.3545195 | 2.060785 | 0.0402 | 0.1714 | 0.04 | 1.43 |
| firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.27 | 0.1351554 | -1.986715 | 0.0479 | 0.1839 | -0.53 | 0.00 |
Genus
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae.g__pseudoramibacter_eubacterium | -2.00 | 0.3808437 | -5.248336 | 0.0000 | 0.0000 | -2.75 | -1.25 |
| proteobacteria.c__epsilonproteobacteria.o__campylobacterales.f__campylobacteraceae.g__campylobacter | 0.96 | 0.2339144 | 4.104901 | 0.0001 | 0.0021 | 0.50 | 1.42 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__.ruminococcus. | 0.57 | 0.1969947 | 2.918040 | 0.0038 | 0.0534 | 0.19 | 0.96 |
| firmicutes.c__bacilli.o__bacillales.f__bacillaceae.g__ | 1.28 | 0.4543072 | 2.816733 | 0.0052 | 0.0534 | 0.39 | 2.17 |
| proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | 0.38 | 0.1332888 | 2.814373 | 0.0052 | 0.0534 | 0.11 | 0.64 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.39 | 0.1410191 | -2.800806 | 0.0054 | 0.0534 | -0.67 | -0.12 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | 0.42 | 0.1610534 | 2.619946 | 0.0093 | 0.0815 | 0.11 | 0.74 |
| proteobacteria.c__gammaproteobacteria.o__aeromonadales.f__aeromonadaceae.g__ | 1.15 | 0.4709164 | 2.447941 | 0.0149 | 0.1164 | 0.23 | 2.08 |
| firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae.g__ | 0.68 | 0.3162457 | 2.144503 | 0.0328 | 0.2244 | 0.06 | 1.30 |
| actinobacteria.c__actinobacteria.o__actinomycetales.f__actinomycetaceae.g__actinomyces | -0.39 | 0.1936470 | -1.988898 | 0.0477 | 0.2528 | -0.76 | -0.01 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.50 | 0.2523901 | 1.976217 | 0.0491 | 0.2528 | 0.00 | 0.99 |
Level 2
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| Metabolism..Glycan.Biosynthesis.and.Metabolism | 0.07 | 0.0163212 | 4.215017 | 0.0000 | 0.0012 | 0.04 | 0.10 |
| Metabolism..Amino.Acid.Metabolism | -0.04 | 0.0096992 | -3.812500 | 0.0002 | 0.0031 | -0.06 | -0.02 |
| Unclassified..Poorly.Characterized | 0.03 | 0.0095207 | 3.424841 | 0.0007 | 0.0069 | 0.01 | 0.05 |
| Unclassified..Metabolism | 0.07 | 0.0203910 | 3.406482 | 0.0007 | 0.0069 | 0.03 | 0.11 |
| Metabolism..Lipid.Metabolism | 0.02 | 0.0058624 | 3.231118 | 0.0014 | 0.0093 | 0.01 | 0.03 |
| Organismal.Systems..Endocrine.System | -0.12 | 0.0361642 | -3.202241 | 0.0015 | 0.0093 | -0.19 | -0.04 |
| Environmental.Information.Processing..Signal.Transduction | 0.12 | 0.0406899 | 3.006687 | 0.0029 | 0.0151 | 0.04 | 0.20 |
| Organismal.Systems..Nervous.System | -0.06 | 0.0221222 | -2.923405 | 0.0037 | 0.0158 | -0.11 | -0.02 |
| Human.Diseases..Infectious.Diseases | 0.05 | 0.0158343 | 2.899207 | 0.0040 | 0.0158 | 0.01 | 0.08 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.09 | 0.0309657 | -2.847834 | 0.0047 | 0.0158 | -0.15 | -0.03 |
| Cellular.Processes..Transport.and.Catabolism | -0.08 | 0.0270700 | -2.829787 | 0.0050 | 0.0158 | -0.13 | -0.02 |
| Unclassified..Cellular.Processes.and.Signaling | 0.08 | 0.0269399 | 2.818421 | 0.0051 | 0.0158 | 0.02 | 0.13 |
| Genetic.Information.Processing..Transcription | 0.02 | 0.0068165 | 2.782895 | 0.0057 | 0.0163 | 0.01 | 0.03 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides | 0.01 | 0.0052916 | 2.572711 | 0.0106 | 0.0272 | 0.00 | 0.02 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites | -0.04 | 0.0156097 | -2.558534 | 0.0110 | 0.0272 | -0.07 | -0.01 |
| Cellular.Processes..Cell.Motility | 0.15 | 0.0607359 | 2.500108 | 0.0129 | 0.0290 | 0.03 | 0.27 |
| Metabolism..Metabolism.of.Other.Amino.Acids | 0.01 | 0.0034517 | 2.489305 | 0.0133 | 0.0290 | 0.00 | 0.02 |
| Human.Diseases..Neurodegenerative.Diseases | 0.09 | 0.0382550 | 2.435313 | 0.0155 | 0.0313 | 0.02 | 0.17 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism | 0.03 | 0.0135599 | 2.420465 | 0.0161 | 0.0313 | 0.01 | 0.06 |
| Genetic.Information.Processing..Replication.and.Repair | -0.03 | 0.0119634 | -2.135868 | 0.0335 | 0.0619 | -0.05 | 0.00 |
| Metabolism..Enzyme.Families | -0.01 | 0.0041515 | -2.080651 | 0.0383 | 0.0675 | -0.02 | 0.00 |
| Cellular.Processes..Cell.Growth.and.Death | -0.03 | 0.0169356 | -2.014184 | 0.0449 | 0.0754 | -0.07 | 0.00 |
| Genetic.Information.Processing..Translation | -0.03 | 0.0164401 | -1.976600 | 0.0490 | 0.0788 | -0.06 | 0.00 |
Level 3
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..C5.Branched.dibasic.acid.metabolism | -0.09 | 0.0214328 | -4.337990 | 0.0000 | 0.0032 | -0.13 | -0.05 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Chaperones.and.folding.catalysts | 0.04 | 0.0097145 | 4.122573 | 0.0000 | 0.0032 | 0.02 | 0.06 |
| Metabolism..Amino.Acid.Metabolism..Phenylalanine..tyrosine.and.tryptophan.biosynthesis | -0.08 | 0.0202757 | -4.075428 | 0.0001 | 0.0032 | -0.12 | -0.04 |
| Metabolism..Amino.Acid.Metabolism..Arginine.and.proline.metabolism | -0.04 | 0.0093143 | -4.042023 | 0.0001 | 0.0032 | -0.06 | -0.02 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.biosynthesis | -0.07 | 0.0177233 | -4.024218 | 0.0001 | 0.0032 | -0.11 | -0.04 |
| Metabolism..Amino.Acid.Metabolism..Glycine..serine.and.threonine.metabolism | -0.04 | 0.0094211 | -3.892352 | 0.0001 | 0.0039 | -0.06 | -0.02 |
| Environmental.Information.Processing..Membrane.Transport..Phosphotransferase.system..PTS. | 0.14 | 0.0359911 | 3.886257 | 0.0001 | 0.0039 | 0.07 | 0.21 |
| Unclassified..Metabolism..Carbohydrate.metabolism | -0.10 | 0.0263032 | -3.856911 | 0.0001 | 0.0039 | -0.15 | -0.05 |
| Metabolism..Amino.Acid.Metabolism..Lysine.biosynthesis | -0.06 | 0.0167669 | -3.782466 | 0.0002 | 0.0046 | -0.10 | -0.03 |
| Unclassified..Cellular.Processes.and.Signaling..Membrane.and.intracellular.structural.molecules | 0.20 | 0.0539469 | 3.734553 | 0.0002 | 0.0048 | 0.10 | 0.31 |
| Metabolism..Amino.Acid.Metabolism..Tyrosine.metabolism | 0.04 | 0.0100122 | 3.717164 | 0.0002 | 0.0048 | 0.02 | 0.06 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis.proteins | 0.29 | 0.0793759 | 3.682344 | 0.0003 | 0.0050 | 0.14 | 0.45 |
| Unclassified..Cellular.Processes.and.Signaling..Pores.ion.channels | 0.21 | 0.0597116 | 3.549333 | 0.0004 | 0.0074 | 0.09 | 0.33 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Thiamine.metabolism | -0.05 | 0.0154782 | -3.535522 | 0.0005 | 0.0074 | -0.09 | -0.02 |
| Environmental.Information.Processing..Membrane.Transport..Transporters | -0.05 | 0.0148166 | -3.511500 | 0.0005 | 0.0076 | -0.08 | -0.02 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Chloroalkane.and.chloroalkene.degradation | -0.07 | 0.0210568 | -3.471330 | 0.0006 | 0.0079 | -0.11 | -0.03 |
| Environmental.Information.Processing..Membrane.Transport..Secretion.system | 0.13 | 0.0378618 | 3.465041 | 0.0006 | 0.0079 | 0.06 | 0.21 |
| Unclassified..Metabolism..Energy.metabolism | 0.13 | 0.0390210 | 3.449100 | 0.0006 | 0.0079 | 0.06 | 0.21 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Glycosyltransferases | 0.16 | 0.0475128 | 3.431370 | 0.0007 | 0.0080 | 0.07 | 0.26 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.09 | 0.0257143 | -3.417511 | 0.0007 | 0.0080 | -0.14 | -0.04 |
| Organismal.Systems..Endocrine.System..PPAR.signaling.pathway | -0.14 | 0.0429330 | -3.373723 | 0.0008 | 0.0089 | -0.23 | -0.06 |
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.08 | 0.0248050 | 3.337006 | 0.0010 | 0.0096 | 0.03 | 0.13 |
| Metabolism..Amino.Acid.Metabolism..Cysteine.and.methionine.metabolism | -0.04 | 0.0134748 | -3.305994 | 0.0011 | 0.0098 | -0.07 | -0.02 |
| Unclassified..Cellular.Processes.and.Signaling..Cell.motility.and.secretion | 0.09 | 0.0285829 | 3.304863 | 0.0011 | 0.0098 | 0.04 | 0.15 |
| Metabolism..Carbohydrate.Metabolism..Starch.and.sucrose.metabolism | -0.08 | 0.0236972 | -3.287954 | 0.0011 | 0.0098 | -0.12 | -0.03 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Riboflavin.metabolism | 0.10 | 0.0296068 | 3.282614 | 0.0011 | 0.0098 | 0.04 | 0.16 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Sulfur.relay.system | 0.14 | 0.0439438 | 3.263629 | 0.0012 | 0.0098 | 0.06 | 0.23 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.18 | 0.0548935 | -3.260450 | 0.0012 | 0.0098 | -0.29 | -0.07 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.06 | 0.0193088 | -3.218336 | 0.0014 | 0.0109 | -0.10 | -0.02 |
| Unclassified..Cellular.Processes.and.Signaling..Other.transporters | 0.12 | 0.0385481 | 3.180404 | 0.0016 | 0.0118 | 0.05 | 0.20 |
| Metabolism..Carbohydrate.Metabolism..Butanoate.metabolism | 0.05 | 0.0166437 | 3.174645 | 0.0017 | 0.0118 | 0.02 | 0.09 |
| Metabolism..Lipid.Metabolism..Glycerophospholipid.metabolism | 0.05 | 0.0166210 | 3.138757 | 0.0019 | 0.0129 | 0.02 | 0.08 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.06 | 0.0197940 | -3.102301 | 0.0021 | 0.0140 | -0.10 | -0.02 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..RNA.degradation | -0.04 | 0.0142902 | -3.082891 | 0.0022 | 0.0140 | -0.07 | -0.02 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Phenylpropanoid.biosynthesis | -0.13 | 0.0410567 | -3.083039 | 0.0022 | 0.0140 | -0.21 | -0.05 |
| Metabolism..Carbohydrate.Metabolism..Propanoate.metabolism | 0.04 | 0.0124717 | 3.066496 | 0.0024 | 0.0140 | 0.01 | 0.06 |
| Unclassified..Poorly.Characterized..General.function.prediction.only | 0.02 | 0.0058957 | 3.062192 | 0.0024 | 0.0140 | 0.01 | 0.03 |
| Genetic.Information.Processing..Replication.and.Repair..Nucleotide.excision.repair | -0.09 | 0.0283217 | -3.061088 | 0.0024 | 0.0140 | -0.14 | -0.03 |
| Environmental.Information.Processing..Signal.Transduction..Two.component.system | 0.14 | 0.0467257 | 3.051950 | 0.0025 | 0.0140 | 0.05 | 0.23 |
| Unclassified..Metabolism..Amino.acid.metabolism | 0.13 | 0.0418094 | 3.042619 | 0.0026 | 0.0141 | 0.05 | 0.21 |
| Metabolism..Lipid.Metabolism..Lipid.biosynthesis.proteins | 0.01 | 0.0048136 | 3.030041 | 0.0027 | 0.0143 | 0.01 | 0.02 |
| Genetic.Information.Processing..Transcription..Transcription.factors | 0.04 | 0.0134457 | 2.997917 | 0.0029 | 0.0155 | 0.01 | 0.07 |
| Metabolism..Metabolism.of.Other.Amino.Acids..beta.Alanine.metabolism | 0.17 | 0.0579307 | 2.979703 | 0.0031 | 0.0160 | 0.06 | 0.29 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction..Bacterial.toxins | -0.14 | 0.0467118 | -2.949014 | 0.0034 | 0.0173 | -0.23 | -0.05 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.08 | 0.0285967 | -2.925386 | 0.0037 | 0.0178 | -0.14 | -0.03 |
| Organismal.Systems..Nervous.System..Glutamatergic.synapse | -0.06 | 0.0221222 | -2.923405 | 0.0037 | 0.0178 | -0.11 | -0.02 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.08 | 0.0284438 | 2.919096 | 0.0038 | 0.0178 | 0.03 | 0.14 |
| Unclassified..Poorly.Characterized..Function.unknown | 0.06 | 0.0198184 | 2.909409 | 0.0039 | 0.0179 | 0.02 | 0.10 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Aminobenzoate.degradation | 0.13 | 0.0458266 | 2.888243 | 0.0042 | 0.0188 | 0.04 | 0.22 |
| Unclassified..Metabolism..Metabolism.of.cofactors.and.vitamins | 0.14 | 0.0473071 | 2.877498 | 0.0043 | 0.0189 | 0.04 | 0.23 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Other.glycan.degradation | -0.15 | 0.0540601 | -2.860084 | 0.0045 | 0.0197 | -0.26 | -0.05 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | 0.13 | 0.0453014 | 2.842982 | 0.0048 | 0.0200 | 0.04 | 0.22 |
| Environmental.Information.Processing..Membrane.Transport..Bacterial.secretion.system | 0.07 | 0.0232601 | 2.841100 | 0.0048 | 0.0200 | 0.02 | 0.11 |
| Cellular.Processes..Cell.Motility..Flagellar.assembly | 0.32 | 0.1157154 | 2.796610 | 0.0055 | 0.0225 | 0.10 | 0.55 |
| Metabolism..Carbohydrate.Metabolism..Glyoxylate.and.dicarboxylate.metabolism | 0.06 | 0.0231906 | 2.766731 | 0.0060 | 0.0242 | 0.02 | 0.11 |
| Metabolism..Lipid.Metabolism..Glycerolipid.metabolism | 0.06 | 0.0220342 | 2.728753 | 0.0067 | 0.0266 | 0.02 | 0.10 |
| Metabolism..Amino.Acid.Metabolism..Alanine..aspartate.and.glutamate.metabolism | -0.04 | 0.0136838 | -2.707962 | 0.0072 | 0.0278 | -0.06 | -0.01 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | 0.07 | 0.0261697 | 2.694539 | 0.0074 | 0.0283 | 0.02 | 0.12 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.04 | 0.0133974 | -2.678519 | 0.0078 | 0.0287 | -0.06 | -0.01 |
| Metabolism..Energy.Metabolism..Carbon.fixation.pathways.in.prokaryotes | 0.02 | 0.0080459 | 2.677095 | 0.0078 | 0.0287 | 0.01 | 0.04 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis | 0.31 | 0.1169356 | 2.672866 | 0.0079 | 0.0287 | 0.08 | 0.54 |
| Unclassified..Cellular.Processes.and.Signaling..Other.ion.coupled.transporters | 0.05 | 0.0188592 | 2.649877 | 0.0085 | 0.0302 | 0.01 | 0.09 |
| Metabolism..Energy.Metabolism..Photosynthesis.proteins | -0.05 | 0.0198840 | -2.632856 | 0.0089 | 0.0312 | -0.09 | -0.01 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.16 | 0.0623648 | -2.617364 | 0.0093 | 0.0322 | -0.29 | -0.04 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Selenocompound.metabolism | -0.03 | 0.0122327 | -2.597275 | 0.0099 | 0.0335 | -0.06 | -0.01 |
| Metabolism..Energy.Metabolism..Photosynthesis | -0.06 | 0.0219419 | -2.584462 | 0.0102 | 0.0342 | -0.10 | -0.01 |
| Cellular.Processes..Cell.Motility..Cytoskeleton.proteins | -0.06 | 0.0231623 | -2.571828 | 0.0106 | 0.0350 | -0.10 | -0.01 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Prenyltransferases | -0.04 | 0.0166380 | -2.553962 | 0.0111 | 0.0361 | -0.08 | -0.01 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Novobiocin.biosynthesis | -0.03 | 0.0126197 | -2.550160 | 0.0113 | 0.0361 | -0.06 | -0.01 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Benzoate.degradation | 0.08 | 0.0327414 | 2.541543 | 0.0115 | 0.0364 | 0.02 | 0.15 |
| Metabolism..Carbohydrate.Metabolism..Citrate.cycle..TCA.cycle. | 0.03 | 0.0126634 | 2.490534 | 0.0133 | 0.0413 | 0.01 | 0.06 |
| Cellular.Processes..Cell.Motility..Bacterial.motility.proteins | 0.19 | 0.0776254 | 2.478104 | 0.0137 | 0.0422 | 0.04 | 0.34 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.05 | 0.0185272 | -2.464623 | 0.0143 | 0.0432 | -0.08 | -0.01 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.04 | 0.0147013 | 2.446898 | 0.0150 | 0.0447 | 0.01 | 0.06 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Streptomycin.biosynthesis | -0.05 | 0.0207643 | -2.442434 | 0.0152 | 0.0447 | -0.09 | -0.01 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.repair.and.recombination.proteins | -0.03 | 0.0115746 | -2.437363 | 0.0154 | 0.0447 | -0.05 | -0.01 |
| Genetic.Information.Processing..Replication.and.Repair..Homologous.recombination | -0.04 | 0.0162049 | -2.422491 | 0.0160 | 0.0459 | -0.07 | -0.01 |
| Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | -0.12 | 0.0495204 | -2.370620 | 0.0184 | 0.0521 | -0.21 | -0.02 |
| Unclassified..Metabolism..Others | 0.03 | 0.0109240 | 2.335657 | 0.0202 | 0.0560 | 0.00 | 0.05 |
| Genetic.Information.Processing..Translation..Aminoacyl.tRNA.biosynthesis | -0.05 | 0.0219340 | -2.333591 | 0.0203 | 0.0560 | -0.09 | -0.01 |
| Environmental.Information.Processing..Membrane.Transport..ABC.transporters | -0.02 | 0.0098570 | -2.298590 | 0.0222 | 0.0600 | -0.04 | 0.00 |
| Metabolism..Energy.Metabolism..Methane.metabolism | -0.02 | 0.0070473 | -2.297401 | 0.0223 | 0.0600 | -0.03 | 0.00 |
| Metabolism..Carbohydrate.Metabolism..Glycolysis…Gluconeogenesis | -0.03 | 0.0114624 | -2.291432 | 0.0226 | 0.0601 | -0.05 | 0.00 |
| Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | 0.03 | 0.0114439 | 2.287667 | 0.0229 | 0.0601 | 0.00 | 0.05 |
| Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.02 | 0.0094755 | 2.268460 | 0.0240 | 0.0624 | 0.00 | 0.04 |
| Genetic.Information.Processing..Translation..Ribosome | -0.05 | 0.0213387 | -2.261201 | 0.0244 | 0.0628 | -0.09 | -0.01 |
| Metabolism..Amino.Acid.Metabolism..Lysine.degradation | 0.13 | 0.0583100 | 2.228455 | 0.0266 | 0.0675 | 0.02 | 0.24 |
| Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | 0.09 | 0.0405700 | 2.217799 | 0.0273 | 0.0686 | 0.01 | 0.17 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.07 | 0.0299017 | 2.213026 | 0.0277 | 0.0687 | 0.01 | 0.12 |
| Metabolism..Carbohydrate.Metabolism..Pyruvate.metabolism | 0.02 | 0.0094877 | 2.161076 | 0.0315 | 0.0773 | 0.00 | 0.04 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Terpenoid.backbone.biosynthesis | -0.04 | 0.0168638 | -2.154288 | 0.0320 | 0.0777 | -0.07 | 0.00 |
| Metabolism..Lipid.Metabolism..Secondary.bile.acid.biosynthesis | -0.15 | 0.0699055 | -2.138006 | 0.0333 | 0.0794 | -0.29 | -0.01 |
| Metabolism..Lipid.Metabolism..Primary.bile.acid.biosynthesis | -0.15 | 0.0697841 | -2.137277 | 0.0334 | 0.0794 | -0.29 | -0.01 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | 0.03 | 0.0160273 | 2.125443 | 0.0343 | 0.0806 | 0.00 | 0.07 |
| Metabolism..Carbohydrate.Metabolism..Galactose.metabolism | -0.05 | 0.0237979 | -2.121521 | 0.0347 | 0.0806 | -0.10 | 0.00 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Glutamine.and.D.glutamate.metabolism | -0.03 | 0.0145028 | -2.099477 | 0.0366 | 0.0842 | -0.06 | 0.00 |
| Genetic.Information.Processing..Transcription..Transcription.machinery | -0.02 | 0.0110271 | -2.091515 | 0.0373 | 0.0850 | -0.04 | 0.00 |
| Unclassified..Genetic.Information.Processing..Restriction.enzyme | -0.08 | 0.0394060 | -2.072812 | 0.0390 | 0.0880 | -0.16 | 0.00 |
| Metabolism..Enzyme.Families..Peptidases | -0.02 | 0.0079776 | -2.044205 | 0.0418 | 0.0927 | -0.03 | 0.00 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.08 | 0.0396205 | 2.042768 | 0.0419 | 0.0927 | 0.00 | 0.16 |
| Unclassified..Cellular.Processes.and.Signaling..Sporulation | -0.15 | 0.0738199 | -2.000512 | 0.0463 | 0.1014 | -0.29 | 0.00 |
Shannon
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 76.8
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 3.3
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 17.8
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 2.2
%W(random)
Subramanian et al 2014 ( Bangladesh ) 76.8
Bender et al 2016 ( Haiti ) 3.3
Pannaraj et al 2017 ( USA(CA_FL) ) 17.8
Thompson et al 2015 ( USA(NC) ) 2.2
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.2681 [0.1448; 0.3914] 4.26 < 0.0001
Random effects model 0.2681 [0.1448; 0.3914] 4.26 < 0.0001
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.94]; I^2 = 0.0% [0.0%; 73.5%]
Test of heterogeneity:
Q d.f. p-value
1.73 3 0.6300
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
Other indexes
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 21.2
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.5
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 74.5
%W(random)
Thompson et al 2015 ( USA(NC) ) 8.9
Pannaraj et al 2017 ( USA(CA_FL) ) 35.4
Bender et al 2016 ( Haiti ) 11.1
Subramanian et al 2014 ( Bangladesh ) 44.6
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.1107 [ 0.0095; 0.2120] 2.14 0.0320
Random effects model 0.1778 [-0.0652; 0.4208] 1.43 0.1515
Quantifying heterogeneity:
tau^2 = 0.0309; H = 1.59 [1.00; 2.76]; I^2 = 60.6% [0.0%; 86.8%]
Test of heterogeneity:
Q d.f. p-value
7.62 3 0.0546
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
Phylum (l2)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes | 0.23 | 0.0929009 | 0.05 | 0.41 | 2.506500 | 0.0122 | 0.1097 |
| k__bacteria.p__firmicutes | 0.18 | 0.0865984 | 0.01 | 0.35 | 2.029901 | 0.0424 | 0.1906 |
Order (l4)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.30 | 0.0877116 | -0.47 | -0.12 | -3.375411 | 0.0007 | 0.0435 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.24 | 0.0930692 | 0.05 | 0.42 | 2.540047 | 0.0111 | 0.1799 |
Family (l5)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__actinobacteria.c__actinobacteria.o__actinomycetales.f__propionibacteriaceae | 10.37 | 0.0096364 | 10.35 | 10.39 | 1076.462007 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.34 | 0.0921764 | 0.16 | 0.52 | 3.729947 | 0.0002 | 0.0088 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.34 | 0.0914966 | -0.52 | -0.16 | -3.708352 | 0.0002 | 0.0088 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.27 | 0.1012548 | 0.07 | 0.47 | 2.644067 | 0.0082 | 0.1936 |
| k__bacteria.p__firmicutes.c__bacilli.o__lactobacillales.f__carnobacteriaceae | -0.32 | 0.1334885 | -0.58 | -0.05 | -2.363485 | 0.0181 | 0.2555 |
Genus (l6)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__actinobacteria.c__actinobacteria.o__actinomycetales.f__propionibacteriaceae.g__propionibacterium | 10.37 | 0.0096364 | 10.35 | 10.39 | 1076.462007 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 3.37 | 0.4299927 | 2.53 | 4.21 | 7.834021 | 0.0000 | 0.0000 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.34 | 0.0919245 | -0.52 | -0.16 | -3.671411 | 0.0002 | 0.0103 |
| k__bacteria.p__proteobacteria.c__betaproteobacteria.o__burkholderiales.f__oxalobacteraceae.g__ralstonia | -1.12 | 0.3911578 | -1.89 | -0.35 | -2.861588 | 0.0042 | 0.1349 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.27 | 0.1012548 | 0.07 | 0.47 | 2.644067 | 0.0082 | 0.2003 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.45 | 0.1719112 | 0.11 | 0.79 | 2.627310 | 0.0086 | 0.2003 |
| k__bacteria.p__firmicutes.c__bacilli.o__lactobacillales.f__carnobacteriaceae.g__granulicatella | -0.32 | 0.1335258 | -0.58 | -0.05 | -2.360386 | 0.0183 | 0.2921 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.35 | 0.1530337 | 0.05 | 0.65 | 2.310869 | 0.0208 | 0.3138 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pseudomonadales.f__pseudomonadaceae.g__pseudomonas | -0.26 | 0.1324610 | -0.52 | 0.00 | -1.981408 | 0.0475 | 0.5506 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Glycan.Biosynthesis.and.Metabolism | 0.05 | 0.0122304 | 0.03 | 0.08 | 4.345847 | 0.0000 | 0.0005 |
| Genetic.Information.Processing..Transcription | 0.02 | 0.0054094 | 0.01 | 0.03 | 3.056402 | 0.0022 | 0.0426 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.06 | 0.0207122 | -0.10 | -0.02 | -2.824348 | 0.0047 | 0.0600 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation | 0.01 | 0.0037159 | 0.00 | 0.02 | 2.221199 | 0.0263 | 0.2502 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites | -0.03 | 0.0125900 | -0.05 | 0.00 | -2.021111 | 0.0433 | 0.3288 |
Level 3 KEGG pathway
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.09 | 0.0177520 | 0.05 | 0.12 | 4.990180 | 0.0000 | 0.0001 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Chaperones.and.folding.catalysts | 0.03 | 0.0071842 | 0.02 | 0.05 | 4.580385 | 0.0000 | 0.0005 |
| Environmental.Information.Processing..Membrane.Transport..Phosphotransferase.system..PTS. | 0.13 | 0.0305596 | 0.07 | 0.19 | 4.219569 | 0.0000 | 0.0019 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.06 | 0.0175651 | -0.10 | -0.03 | -3.631992 | 0.0003 | 0.0162 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.06 | 0.0192851 | -0.10 | -0.02 | -2.985966 | 0.0028 | 0.1300 |
| Organismal.Systems..Endocrine.System..PPAR.signaling.pathway | -0.10 | 0.0353891 | -0.17 | -0.03 | -2.746360 | 0.0060 | 0.2133 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | 0.0269951 | -0.13 | -0.02 | -2.721881 | 0.0065 | 0.2133 |
| Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | 0.02 | 0.0091880 | 0.01 | 0.04 | 2.534213 | 0.0113 | 0.2827 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.03 | 0.0118755 | 0.01 | 0.05 | 2.492261 | 0.0127 | 0.2827 |
| Unclassified..Cellular.Processes.and.Signaling..Other.ion.coupled.transporters | 0.03 | 0.0124677 | 0.01 | 0.06 | 2.470926 | 0.0135 | 0.2827 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.03 | 0.0106104 | -0.05 | -0.01 | -2.460078 | 0.0139 | 0.2827 |
| Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.02 | 0.0088373 | 0.00 | 0.04 | 2.411772 | 0.0159 | 0.2827 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.05 | 0.0214619 | 0.01 | 0.09 | 2.409349 | 0.0160 | 0.2827 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.11 | 0.0543425 | -0.22 | -0.01 | -2.104930 | 0.0353 | 0.5799 |
| id | Estimate.bfNon_exclusiveBF | Std. Error.bfNon_exclusiveBF | t value.bfNon_exclusiveBF | Pr(>|t|).bfNon_exclusiveBF |
|---|---|---|---|---|
| chao1 | 0.07 | 0.04 | 1.66 | 0.0961 |
| observed_species | 0.07 | 0.04 | 1.69 | 0.0905 |
| pd_whole_tree | 0.10 | 0.04 | 2.49 | 0.0127 |
| shannon | 0.26 | 0.07 | 3.58 | 0.0003 |
| Estimate | Std. Error | df | t value | Pr(>|t|) | varname | pop | |
|---|---|---|---|---|---|---|---|
| bfNo_BF | -0.1075706 | 0.1666272 | 248.75546 | -0.6455766 | 0.5191486 | bfNo_BF | Bangladesh |
| bfNon_exclusiveBF | 0.0339266 | 0.0571267 | 202.03700 | 0.5938845 | 0.5532537 | bfNon_exclusiveBF | Bangladesh |
| genderMale | -0.0909496 | 0.0595166 | 36.06456 | -1.5281378 | 0.1352025 | genderMale | Bangladesh |
| age.sample | 0.0862128 | 0.0136845 | 236.02555 | 6.3000537 | 0.0000000 | age.sample | Bangladesh |
phylum
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 5 | k__bacteria.p__proteobacteria | 0.37 | 0.11 | 0.63 | 0.0061 | 0.0448 |
| 1 | k__bacteria.p__actinobacteria | -0.37 | -0.64 | -0.10 | 0.0086 | 0.0590 |
| 3 | k__bacteria.p__firmicutes | 0.24 | 0.01 | 0.46 | 0.0428 | 0.1767 |
order
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 26 | k__bacteria.p__proteobacteria.c__epsilonproteobacteria.o__campylobacterales | 0.92 | 0.47 | 1.36 | 0.0001 | 0.0015 |
| 28 | k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales | 0.37 | 0.11 | 0.64 | 0.0057 | 0.0448 |
| 17 | k__bacteria.p__actinobacteria.c__actinobacteria.o__bifidobacteriales | -0.39 | -0.67 | -0.12 | 0.0057 | 0.0448 |
| 22 | k__bacteria.p__firmicutes.c__bacilli.o__lactobacillales | 0.25 | 0.01 | 0.48 | 0.0380 | 0.1728 |
| 18 | k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales | 0.27 | 0.02 | 0.53 | 0.0386 | 0.1728 |
family
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 51 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae | -2.06 | -2.95 | -1.17 | 0.0000 | 0.0005 |
| 59 | k__bacteria.p__proteobacteria.c__epsilonproteobacteria.o__campylobacterales.f__campylobacteraceae | 0.96 | 0.50 | 1.41 | 0.0001 | 0.0015 |
| 61 | k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | 0.37 | 0.11 | 0.64 | 0.0057 | 0.0448 |
| 34 | k__bacteria.p__actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.39 | -0.67 | -0.12 | 0.0057 | 0.0448 |
| 60 | k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__aeromonadales.f__aeromonadaceae | 1.15 | 0.22 | 2.09 | 0.0159 | 0.0920 |
| 35 | k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | 0.27 | 0.02 | 0.53 | 0.0386 | 0.1728 |
| 42 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.27 | -0.52 | -0.01 | 0.0402 | 0.1728 |
| 37 | k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__porphyromonadaceae | 0.73 | 0.04 | 1.43 | 0.0404 | 0.1728 |
genus
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 93 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae.g__pseudoramibacter_eubacterium | -2.06 | -2.95 | -1.17 | 0.0000 | 0.0005 |
| 116 | k__bacteria.p__proteobacteria.c__epsilonproteobacteria.o__campylobacterales.f__campylobacteraceae.g__campylobacter | 0.96 | 0.50 | 1.41 | 0.0001 | 0.0015 |
| 78 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__bacillaceae.g__ | 1.28 | 0.44 | 2.12 | 0.0030 | 0.0448 |
| 99 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__.ruminococcus. | 0.59 | 0.18 | 1.00 | 0.0050 | 0.0448 |
| 69 | k__bacteria.p__actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.39 | -0.67 | -0.12 | 0.0057 | 0.0448 |
| 119 | k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | 0.37 | 0.11 | 0.63 | 0.0060 | 0.0448 |
| 100 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae.g__ | 0.68 | 0.17 | 1.19 | 0.0092 | 0.0601 |
| 70 | k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | 0.41 | 0.09 | 0.73 | 0.0118 | 0.0731 |
| 117 | k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__aeromonadales.f__aeromonadaceae.g__ | 1.15 | 0.22 | 2.08 | 0.0163 | 0.0920 |
| 64 | k__bacteria.p__actinobacteria.c__actinobacteria.o__actinomycetales.f__actinomycetaceae.g__actinomyces | -0.39 | -0.73 | -0.05 | 0.0274 | 0.1477 |
| 80 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.26 | -0.52 | -0.01 | 0.0449 | 0.1795 |
Level 2
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 16 | Metabolism..Glycan.Biosynthesis.and.Metabolism | 0.07 | 0.04 | 0.10 | 0.0000 | 0.0013 |
| 1 | Metabolism..Amino.Acid.Metabolism | -0.04 | -0.06 | -0.02 | 0.0002 | 0.0036 |
| 30 | Unclassified..Poorly.Characterized | 0.03 | 0.01 | 0.05 | 0.0008 | 0.0083 |
| 23 | Unclassified..Metabolism | 0.07 | 0.03 | 0.11 | 0.0009 | 0.0083 |
| 20 | Metabolism..Lipid.Metabolism | 0.02 | 0.01 | 0.03 | 0.0016 | 0.0103 |
| 9 | Organismal.Systems..Endocrine.System | -0.12 | -0.19 | -0.04 | 0.0017 | 0.0103 |
| 32 | Environmental.Information.Processing..Signal.Transduction | 0.12 | 0.04 | 0.20 | 0.0034 | 0.0177 |
| 27 | Organismal.Systems..Nervous.System | -0.06 | -0.11 | -0.02 | 0.0042 | 0.0177 |
| 19 | Human.Diseases..Infectious.Diseases | 0.05 | 0.01 | 0.08 | 0.0043 | 0.0177 |
| 33 | Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.09 | -0.15 | -0.03 | 0.0055 | 0.0187 |
| 36 | Cellular.Processes..Transport.and.Catabolism | -0.08 | -0.13 | -0.02 | 0.0057 | 0.0187 |
| 7 | Unclassified..Cellular.Processes.and.Signaling | 0.07 | 0.02 | 0.13 | 0.0061 | 0.0187 |
| 34 | Genetic.Information.Processing..Transcription | 0.02 | 0.01 | 0.03 | 0.0067 | 0.0192 |
| 2 | Metabolism..Biosynthesis.of.Other.Secondary.Metabolites | -0.04 | -0.07 | -0.01 | 0.0117 | 0.0307 |
| 26 | Metabolism..Metabolism.of.Terpenoids.and.Polyketides | 0.01 | 0.00 | 0.02 | 0.0124 | 0.0307 |
| 25 | Metabolism..Metabolism.of.Other.Amino.Acids | 0.01 | 0.00 | 0.02 | 0.0145 | 0.0335 |
| 6 | Cellular.Processes..Cell.Motility | 0.15 | 0.03 | 0.27 | 0.0154 | 0.0335 |
| 28 | Human.Diseases..Neurodegenerative.Diseases | 0.09 | 0.02 | 0.17 | 0.0174 | 0.0344 |
| 37 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism | 0.03 | 0.01 | 0.06 | 0.0177 | 0.0344 |
| 31 | Genetic.Information.Processing..Replication.and.Repair | -0.03 | -0.05 | 0.00 | 0.0375 | 0.0693 |
| 12 | Metabolism..Enzyme.Families | -0.01 | -0.02 | 0.00 | 0.0417 | 0.0735 |
Level 3
| id | Estimate.bfNon_exclusiveBF | ll | ul | Pr(>|t|).bfNon_exclusiveBF | pval.adjust.bfNon_exclusiveBF | |
|---|---|---|---|---|---|---|
| 33 | Metabolism..Carbohydrate.Metabolism..C5.Branched.dibasic.acid.metabolism | -0.09 | -0.13 | -0.05 | 0.0000 | 0.0038 |
| 44 | Genetic.Information.Processing..Folding..Sorting.and.Degradation..Chaperones.and.folding.catalysts | 0.04 | 0.02 | 0.06 | 0.0001 | 0.0038 |
| 139 | Metabolism..Amino.Acid.Metabolism..Phenylalanine..tyrosine.and.tryptophan.biosynthesis | -0.08 | -0.12 | -0.04 | 0.0001 | 0.0038 |
| 15 | Metabolism..Amino.Acid.Metabolism..Arginine.and.proline.metabolism | -0.04 | -0.06 | -0.02 | 0.0001 | 0.0038 |
| 213 | Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.biosynthesis | -0.07 | -0.11 | -0.04 | 0.0001 | 0.0040 |
| 81 | Metabolism..Amino.Acid.Metabolism..Glycine..serine.and.threonine.metabolism | -0.04 | -0.05 | -0.02 | 0.0001 | 0.0046 |
| 143 | Environmental.Information.Processing..Membrane.Transport..Phosphotransferase.system..PTS. | 0.14 | 0.07 | 0.21 | 0.0002 | 0.0046 |
| 36 | Unclassified..Metabolism..Carbohydrate.metabolism | -0.10 | -0.15 | -0.05 | 0.0002 | 0.0046 |
| 103 | Metabolism..Amino.Acid.Metabolism..Lysine.biosynthesis | -0.06 | -0.10 | -0.03 | 0.0002 | 0.0054 |
| 108 | Unclassified..Cellular.Processes.and.Signaling..Membrane.and.intracellular.structural.molecules | 0.20 | 0.09 | 0.31 | 0.0003 | 0.0058 |
| 102 | Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis.proteins | 0.29 | 0.13 | 0.45 | 0.0003 | 0.0064 |
| 210 | Metabolism..Amino.Acid.Metabolism..Tyrosine.metabolism | 0.04 | 0.02 | 0.06 | 0.0004 | 0.0069 |
| 149 | Unclassified..Cellular.Processes.and.Signaling..Pores.ion.channels | 0.21 | 0.09 | 0.33 | 0.0005 | 0.0086 |
| 196 | Metabolism..Metabolism.of.Cofactors.and.Vitamins..Thiamine.metabolism | -0.05 | -0.08 | -0.02 | 0.0006 | 0.0086 |
| 203 | Environmental.Information.Processing..Membrane.Transport..Transporters | -0.05 | -0.08 | -0.02 | 0.0007 | 0.0086 |
| 45 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Chloroalkane.and.chloroalkene.degradation | -0.07 | -0.11 | -0.03 | 0.0007 | 0.0086 |
| 181 | Environmental.Information.Processing..Membrane.Transport..Secretion.system | 0.13 | 0.06 | 0.20 | 0.0007 | 0.0086 |
| 61 | Unclassified..Metabolism..Energy.metabolism | 0.13 | 0.06 | 0.21 | 0.0007 | 0.0086 |
| 86 | Metabolism..Glycan.Biosynthesis.and.Metabolism..Glycosyltransferases | 0.16 | 0.07 | 0.26 | 0.0007 | 0.0086 |
| 136 | Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.09 | -0.14 | -0.04 | 0.0009 | 0.0095 |
| 128 | Organismal.Systems..Endocrine.System..PPAR.signaling.pathway | -0.14 | -0.23 | -0.06 | 0.0010 | 0.0101 |
| 70 | Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.08 | 0.03 | 0.13 | 0.0012 | 0.0111 |
| 176 | Metabolism..Metabolism.of.Cofactors.and.Vitamins..Riboflavin.metabolism | 0.10 | 0.04 | 0.16 | 0.0013 | 0.0111 |
| 50 | Metabolism..Amino.Acid.Metabolism..Cysteine.and.methionine.metabolism | -0.04 | -0.07 | -0.02 | 0.0013 | 0.0111 |
| 41 | Unclassified..Cellular.Processes.and.Signaling..Cell.motility.and.secretion | 0.09 | 0.04 | 0.15 | 0.0013 | 0.0111 |
| 187 | Metabolism..Carbohydrate.Metabolism..Starch.and.sucrose.metabolism | -0.08 | -0.12 | -0.03 | 0.0013 | 0.0111 |
| 191 | Genetic.Information.Processing..Folding..Sorting.and.Degradation..Sulfur.relay.system | 0.14 | 0.06 | 0.23 | 0.0014 | 0.0116 |
| 2 | Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.18 | -0.28 | -0.07 | 0.0015 | 0.0116 |
| 116 | Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.06 | -0.10 | -0.02 | 0.0017 | 0.0127 |
| 125 | Unclassified..Cellular.Processes.and.Signaling..Other.transporters | 0.12 | 0.05 | 0.20 | 0.0019 | 0.0138 |
| 31 | Metabolism..Carbohydrate.Metabolism..Butanoate.metabolism | 0.05 | 0.02 | 0.09 | 0.0019 | 0.0138 |
| 140 | Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Phenylpropanoid.biosynthesis | -0.13 | -0.21 | -0.05 | 0.0021 | 0.0145 |
| 80 | Metabolism..Lipid.Metabolism..Glycerophospholipid.metabolism | 0.05 | 0.02 | 0.08 | 0.0022 | 0.0145 |
| 169 | Genetic.Information.Processing..Folding..Sorting.and.Degradation..RNA.degradation | -0.04 | -0.07 | -0.02 | 0.0026 | 0.0160 |
| 217 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.06 | -0.10 | -0.02 | 0.0027 | 0.0160 |
| 156 | Metabolism..Carbohydrate.Metabolism..Propanoate.metabolism | 0.04 | 0.01 | 0.06 | 0.0027 | 0.0160 |
| 73 | Unclassified..Poorly.Characterized..General.function.prediction.only | 0.02 | 0.01 | 0.03 | 0.0028 | 0.0160 |
| 120 | Genetic.Information.Processing..Replication.and.Repair..Nucleotide.excision.repair | -0.09 | -0.14 | -0.03 | 0.0028 | 0.0160 |
| 6 | Unclassified..Metabolism..Amino.acid.metabolism | 0.13 | 0.04 | 0.21 | 0.0028 | 0.0160 |
| 207 | Environmental.Information.Processing..Signal.Transduction..Two.component.system | 0.14 | 0.05 | 0.23 | 0.0030 | 0.0164 |
| 98 | Metabolism..Lipid.Metabolism..Lipid.biosynthesis.proteins | 0.01 | 0.00 | 0.02 | 0.0030 | 0.0164 |
| 198 | Genetic.Information.Processing..Transcription..Transcription.factors | 0.04 | 0.01 | 0.07 | 0.0034 | 0.0181 |
| 220 | Metabolism..Metabolism.of.Other.Amino.Acids..beta.Alanine.metabolism | 0.17 | 0.06 | 0.29 | 0.0035 | 0.0181 |
| 21 | Environmental.Information.Processing..Signaling.Molecules.and.Interaction..Bacterial.toxins | -0.14 | -0.23 | -0.04 | 0.0039 | 0.0197 |
| 76 | Organismal.Systems..Nervous.System..Glutamatergic.synapse | -0.06 | -0.11 | -0.02 | 0.0042 | 0.0201 |
| 179 | Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.08 | -0.14 | -0.03 | 0.0042 | 0.0201 |
| 65 | Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.08 | 0.03 | 0.14 | 0.0043 | 0.0201 |
| 71 | Unclassified..Poorly.Characterized..Function.unknown | 0.06 | 0.02 | 0.10 | 0.0047 | 0.0211 |
| 123 | Metabolism..Glycan.Biosynthesis.and.Metabolism..Other.glycan.degradation | -0.15 | -0.26 | -0.05 | 0.0047 | 0.0211 |
| 10 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Aminobenzoate.degradation | 0.13 | 0.04 | 0.22 | 0.0048 | 0.0211 |
| 109 | Unclassified..Metabolism..Metabolism.of.cofactors.and.vitamins | 0.13 | 0.04 | 0.23 | 0.0052 | 0.0226 |
| 96 | Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | 0.13 | 0.04 | 0.22 | 0.0056 | 0.0236 |
| 20 | Environmental.Information.Processing..Membrane.Transport..Bacterial.secretion.system | 0.07 | 0.02 | 0.11 | 0.0057 | 0.0238 |
| 67 | Cellular.Processes..Cell.Motility..Flagellar.assembly | 0.32 | 0.09 | 0.55 | 0.0061 | 0.0248 |
| 87 | Metabolism..Carbohydrate.Metabolism..Glyoxylate.and.dicarboxylate.metabolism | 0.06 | 0.02 | 0.11 | 0.0067 | 0.0269 |
| 79 | Metabolism..Lipid.Metabolism..Glycerolipid.metabolism | 0.06 | 0.02 | 0.10 | 0.0077 | 0.0304 |
| 4 | Metabolism..Amino.Acid.Metabolism..Alanine..aspartate.and.glutamate.metabolism | -0.04 | -0.06 | -0.01 | 0.0081 | 0.0307 |
| 214 | Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | 0.07 | 0.02 | 0.12 | 0.0083 | 0.0307 |
| 101 | Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis | 0.31 | 0.08 | 0.54 | 0.0083 | 0.0307 |
| 38 | Metabolism..Energy.Metabolism..Carbon.fixation.pathways.in.prokaryotes | 0.02 | 0.01 | 0.04 | 0.0083 | 0.0307 |
| 216 | Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.04 | -0.06 | -0.01 | 0.0091 | 0.0329 |
| 158 | Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.16 | -0.29 | -0.04 | 0.0098 | 0.0349 |
| 124 | Unclassified..Cellular.Processes.and.Signaling..Other.ion.coupled.transporters | 0.05 | 0.01 | 0.09 | 0.0101 | 0.0355 |
| 145 | Metabolism..Energy.Metabolism..Photosynthesis.proteins | -0.05 | -0.09 | -0.01 | 0.0105 | 0.0361 |
| 182 | Metabolism..Metabolism.of.Other.Amino.Acids..Selenocompound.metabolism | -0.03 | -0.06 | -0.01 | 0.0112 | 0.0380 |
| 144 | Metabolism..Energy.Metabolism..Photosynthesis | -0.06 | -0.10 | -0.01 | 0.0119 | 0.0397 |
| 51 | Cellular.Processes..Cell.Motility..Cytoskeleton.proteins | -0.06 | -0.10 | -0.01 | 0.0120 | 0.0397 |
| 151 | Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Prenyltransferases | -0.04 | -0.07 | -0.01 | 0.0126 | 0.0408 |
| 23 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Benzoate.degradation | 0.08 | 0.02 | 0.15 | 0.0128 | 0.0408 |
| 119 | Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Novobiocin.biosynthesis | -0.03 | -0.06 | -0.01 | 0.0129 | 0.0408 |
| 48 | Metabolism..Carbohydrate.Metabolism..Citrate.cycle..TCA.cycle. | 0.03 | 0.01 | 0.06 | 0.0141 | 0.0440 |
| 19 | Cellular.Processes..Cell.Motility..Bacterial.motility.proteins | 0.19 | 0.04 | 0.34 | 0.0160 | 0.0487 |
| 52 | Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.04 | 0.01 | 0.06 | 0.0161 | 0.0487 |
| 66 | Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.04 | -0.08 | -0.01 | 0.0171 | 0.0505 |
| 188 | Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Streptomycin.biosynthesis | -0.05 | -0.09 | -0.01 | 0.0172 | 0.0505 |
| 54 | Genetic.Information.Processing..Replication.and.Repair..DNA.repair.and.recombination.proteins | -0.03 | -0.05 | 0.00 | 0.0177 | 0.0514 |
| 89 | Genetic.Information.Processing..Replication.and.Repair..Homologous.recombination | -0.04 | -0.07 | -0.01 | 0.0183 | 0.0526 |
| 184 | Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | -0.12 | -0.21 | -0.02 | 0.0198 | 0.0560 |
| 9 | Genetic.Information.Processing..Translation..Aminoacyl.tRNA.biosynthesis | -0.05 | -0.09 | -0.01 | 0.0233 | 0.0651 |
| 126 | Unclassified..Metabolism..Others | 0.02 | 0.00 | 0.05 | 0.0236 | 0.0651 |
| 111 | Metabolism..Energy.Metabolism..Methane.metabolism | -0.02 | -0.03 | 0.00 | 0.0246 | 0.0672 |
| 183 | Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | 0.03 | 0.00 | 0.05 | 0.0258 | 0.0694 |
| 82 | Metabolism..Carbohydrate.Metabolism..Glycolysis…Gluconeogenesis | -0.03 | -0.05 | 0.00 | 0.0261 | 0.0694 |
| 177 | Genetic.Information.Processing..Translation..Ribosome | -0.05 | -0.09 | -0.01 | 0.0280 | 0.0730 |
| 141 | Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.02 | 0.00 | 0.04 | 0.0281 | 0.0730 |
| 1 | Environmental.Information.Processing..Membrane.Transport..ABC.transporters | -0.02 | -0.04 | 0.00 | 0.0292 | 0.0748 |
| 104 | Metabolism..Amino.Acid.Metabolism..Lysine.degradation | 0.13 | 0.01 | 0.24 | 0.0297 | 0.0748 |
| 132 | Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.07 | 0.01 | 0.12 | 0.0298 | 0.0748 |
| 205 | Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | 0.09 | 0.01 | 0.17 | 0.0306 | 0.0760 |
| 167 | Metabolism..Carbohydrate.Metabolism..Pyruvate.metabolism | 0.02 | 0.00 | 0.04 | 0.0350 | 0.0851 |
| 180 | Metabolism..Lipid.Metabolism..Secondary.bile.acid.biosynthesis | -0.15 | -0.29 | -0.01 | 0.0354 | 0.0851 |
| 152 | Metabolism..Lipid.Metabolism..Primary.bile.acid.biosynthesis | -0.15 | -0.28 | -0.01 | 0.0354 | 0.0851 |
| 194 | Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Terpenoid.backbone.biosynthesis | -0.04 | -0.07 | 0.00 | 0.0358 | 0.0851 |
| 72 | Metabolism..Carbohydrate.Metabolism..Galactose.metabolism | -0.05 | -0.10 | 0.00 | 0.0389 | 0.0906 |
| 199 | Genetic.Information.Processing..Transcription..Transcription.machinery | -0.02 | -0.04 | 0.00 | 0.0390 | 0.0906 |
| 77 | Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | 0.03 | 0.00 | 0.06 | 0.0397 | 0.0914 |
| 53 | Metabolism..Metabolism.of.Other.Amino.Acids..D.Glutamine.and.D.glutamate.metabolism | -0.03 | -0.06 | 0.00 | 0.0406 | 0.0926 |
| 174 | Unclassified..Genetic.Information.Processing..Restriction.enzyme | -0.08 | -0.16 | 0.00 | 0.0446 | 0.1003 |
| 29 | Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.08 | 0.00 | 0.16 | 0.0449 | 0.1003 |
| 134 | Metabolism..Enzyme.Families..Peptidases | -0.02 | -0.03 | 0.00 | 0.0459 | 0.1013 |
| 185 | Unclassified..Cellular.Processes.and.Signaling..Sporulation | -0.15 | -0.29 | 0.00 | 0.0472 | 0.1034 |
RD 95%-CI %W(fixed) %W(random)
Bangladesh 0.2582 [ 0.1168; 0.3996] 78.0 78.0
Haiti -0.1128 [-0.8117; 0.5861] 3.2 3.2
USA(CA_FL) 0.3297 [ 0.0264; 0.6331] 17.0 17.0
USA(UNC) 0.2898 [-0.6376; 1.2172] 1.8 1.8
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.2591 [0.1342; 0.3840] 4.07 < 0.0001
Random effects model 0.2591 [0.1342; 0.3840] 4.07 < 0.0001
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.68]; I^2 = 0.0% [0.0%; 64.7%]
Test of heterogeneity:
Q d.f. p-value
1.30 3 0.7291
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Bangladesh | 0.000344378476206655 |
| Haiti | 0.751832160135333 |
| USA(CA_FL) | 0.033139645082754 |
| USA(UNC) | 0.540228852041577 |
Other indexes
RD 95%-CI %W(fixed)
Subramanian et al 2014 (Bangladesh) 0.0466 [-0.0707; 0.1639] 74.1
Bender et al 2016 (Haiti) -0.3112 [-0.9449; 0.3224] 2.5
Pannaraj et al 2017 (USA(CA_FL)) 0.2476 [ 0.0253; 0.4699] 20.6
Thompson et al 2015 (USA(NC)) 1.0076 [ 0.3937; 1.6215] 2.7
%W(random)
Subramanian et al 2014 (Bangladesh) 37.3
Bender et al 2016 (Haiti) 14.7
Pannaraj et al 2017 (USA(CA_FL)) 32.7
Thompson et al 2015 (USA(NC)) 15.3
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.1050 [ 0.0040; 0.2060] 2.04 0.0416
Random effects model 0.2066 [-0.1000; 0.5133] 1.32 0.1865
Quantifying heterogeneity:
tau^2 = 0.0620; H = 2.04 [1.23; 3.39]; I^2 = 76.0% [33.9%; 91.3%]
Test of heterogeneity:
Q d.f. p-value
12.50 3 0.0059
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 (Bangladesh) | 0.436137583408132 |
| Bender et al 2016 (Haiti) | 0.335677203059515 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.0290537069289293 |
| Thompson et al 2015 (USA(NC)) | 0.00129477371396216 |
phylum
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 2 | k__bacteria.p__bacteroidetes | 0.25 | 0.05 | 0.45 | 0.0123 | 0.3952 |
| 3 | k__bacteria.p__firmicutes | 0.18 | 0.01 | 0.35 | 0.0399 | 0.4183 |
order
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 24 | k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.31 | 0.06 | 0.56 | 0.0150 | 0.3952 |
| 19 | k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.24 | 0.04 | 0.43 | 0.0184 | 0.3952 |
| 18 | k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales | 0.22 | 0.02 | 0.42 | 0.0310 | 0.3963 |
| 20 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.19 | -0.37 | -0.02 | 0.0328 | 0.3963 |
family
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 54 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.25 | 0.06 | 0.43 | 0.0080 | 0.3952 |
| 56 | k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.31 | 0.06 | 0.56 | 0.0150 | 0.3952 |
| 42 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.23 | -0.43 | -0.03 | 0.0226 | 0.3952 |
| 35 | k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | 0.22 | 0.02 | 0.42 | 0.0310 | 0.3963 |
genus
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 167 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 2.89 | 1.68 | 4.10 | 0.0000 | 0.0005 |
| 102 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.22 | 0.03 | 0.41 | 0.0208 | 0.3952 |
| 77 | k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.23 | -0.43 | -0.03 | 0.0235 | 0.3952 |
| 93 | k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__.ruminococcus. | 0.31 | 0.02 | 0.61 | 0.0343 | 0.3963 |
| 106 | k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__ | 0.31 | 0.01 | 0.61 | 0.0407 | 0.4183 |
Level 2
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 34 | Genetic.Information.Processing..Transcription | 0.02 | 0.01 | 0.03 | 0.0045 | 0.1723 |
Level 3
| id | estimate | ll | ul | p | p.adjust | |
|---|---|---|---|---|---|---|
| 143 | Environmental.Information.Processing..Membrane.Transport..Phosphotransferase.system..PTS. | 0.13 | 0.07 | 0.19 | 0.0000 | 0.0108 |
| 217 | Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.06 | -0.10 | -0.02 | 0.0029 | 0.3354 |
| 179 | Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.07 | -0.13 | -0.02 | 0.0068 | 0.3635 |
| 70 | Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.10 | 0.03 | 0.18 | 0.0079 | 0.3635 |
| 198 | Genetic.Information.Processing..Transcription..Transcription.factors | 0.03 | 0.01 | 0.06 | 0.0079 | 0.3635 |
| 141 | Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.02 | 0.00 | 0.04 | 0.0171 | 0.6543 |
| 158 | Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.12 | -0.23 | -0.01 | 0.0274 | 0.8997 |
| 183 | Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | 0.02 | 0.00 | 0.04 | 0.0367 | 0.9981 |
| 1 | Environmental.Information.Processing..Membrane.Transport..ABC.transporters | -0.02 | -0.04 | 0.00 | 0.0402 | 0.9981 |
R session information
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] metamicrobiomeR_1.0 devtools_1.13.5 gplots_3.0.1
[4] bindrcpp_0.2.2 meta_4.9-2 randomForest_4.6-14
[7] gdata_2.18.0 scales_0.5.0 wesanderson_0.3.6
[10] RColorBrewer_1.1-2 geepack_1.2-1 zoo_1.8-0
[13] itsadug_2.3 plotfunctions_1.3 mgcv_1.8-22
[16] nlme_3.1-131 reshape2_1.4.3 lmerTest_3.0-1
[19] sjPlot_2.4.0 sjmisc_2.6.3 lme4_1.1-17
[22] Matrix_1.2-12 tidyr_0.7.2 dtplyr_0.0.2
[25] data.table_1.10.4-3 dplyr_0.7.6 date_1.2-37
[28] lubridate_1.7.1 chron_2.3-51 gmodels_2.16.2
[31] gridExtra_2.3 plyr_1.8.4 digest_0.6.12
[34] caret_6.0-80 ggplot2_2.2.1 lattice_0.20-35
[37] knitr_1.20
loaded via a namespace (and not attached):
[1] backports_1.1.1 blme_1.0-4 lazyeval_0.2.1
[4] TMB_1.7.11 splines_3.4.2 TH.data_1.0-8
[7] foreach_1.4.3 htmltools_0.3.6 memoise_1.1.0
[10] magrittr_1.5 sfsmisc_1.1-1 recipes_0.1.1
[13] modelr_0.1.1 gower_0.1.2 dimRed_0.1.0
[16] sandwich_2.4-0 colorspace_1.3-2 haven_1.1.0
[19] crayon_1.3.4 bindr_0.1.1 survival_2.41-3
[22] iterators_1.0.8 glue_1.2.0 DRR_0.0.2
[25] gtable_0.2.0 ipred_0.9-6 sjstats_0.13.0
[28] kernlab_0.9-25 ddalpha_1.3.1 DEoptimR_1.0-8
[31] abind_1.4-5 mvtnorm_1.0-6 ggeffects_0.3.0
[34] Rcpp_0.12.17 xtable_1.8-2 merTools_0.3.0
[37] foreign_0.8-69 stats4_3.4.2 prediction_0.2.0
[40] lava_1.5.1 survey_3.32-1 prodlim_1.6.1
[43] DT_0.2 httr_1.3.1 htmlwidgets_0.9
[46] modeltools_0.2-21 pkgconfig_2.0.1 nnet_7.3-12
[49] tidyselect_0.2.3 labeling_0.3 rlang_0.2.1
[52] munsell_0.4.3 tools_3.4.2 cli_1.0.0
[55] sjlabelled_1.0.5 broom_0.4.3 evaluate_0.10.1
[58] stringr_1.2.0 arm_1.9-3 yaml_2.1.15
[61] ModelMetrics_1.1.0 robustbase_0.92-8 caTools_1.17.1
[64] purrr_0.2.4 coin_1.2-2 mime_0.5
[67] RcppRoll_0.2.2 compiler_3.4.2 bayesplot_1.4.0
[70] curl_3.0 tibble_1.3.4 stringi_1.1.6
[73] highr_0.6 forcats_0.2.0 psych_1.7.8
[76] nloptr_1.0.4 effects_4.0-0 stringdist_0.9.4.6
[79] pwr_1.2-1 lmtest_0.9-35 bitops_1.0-6
[82] httpuv_1.3.5 R6_2.2.2 KernSmooth_2.23-15
[85] codetools_0.2-15 MASS_7.3-47 gtools_3.5.0
[88] assertthat_0.2.0 CVST_0.2-1 rprojroot_1.2
[91] withr_2.1.0 mnormt_1.5-5 multcomp_1.4-8
[94] parallel_3.4.2 grid_3.4.2 rpart_4.1-11
[97] timeDate_3042.101 coda_0.19-1 glmmTMB_0.2.0
[100] class_7.3-14 minqa_1.2.4 rmarkdown_1.10
[103] snakecase_0.5.1 carData_3.0-0 git2r_0.19.0
[106] numDeriv_2016.8-1 shiny_1.0.5